Chicken_Neuroendocrine_System

TomEricPorter TomEPorter LEEllestad MMuchow SAJenkins WCarre LarryACogburn LauraEEllestad WilfridCarre MichaelMuchow SultanAJenkins XiaofeiWang Gene Expression Omnibus (GEO)

GEO

NCBI NLM NIH

http://www.ncbi.nlm.nih.gov/geo

geo@ncbi.nlm.nih.gov Chicken_Neuroendocrine_System_5K spotted DNA/cDNA non-commercial Gallus gallus Delaware Biotechnology Institute and University of Maryland

Spotted amplified cDNA array on glass. Produced with cDNA clones expressed in the chicken neuroendocrine system. Tissues used to produced the cDNA library included the hypothalamus, anterior pituitary gland, and pineal gland. PCR products were re-arrayed into 384-well plates in 50% DMSO and printed onto glass microscope slides (Full Moon Biosystems; Sunnyvale, CA) as high-density cDNA microarrays at the Delaware Biotechnology Institute (http://www.dbi.udel.edu/) using the OmniGrid 100 arrayer (Genomic Solutions, Ann Arbor, MI).

Glass

http://www.ansc.umd.edu/faculty/tpresearch.htm

ID CLONE_NAME GB_ACC GenBank accession number of sequence

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=

BLAST_X First BlastX result BLAST_N First BlastN result CAP3_ASSEMBLY Result of CAP3 Assembly

http://www.chickest.udel.edu/Cogburn_CAP3_DB/Diagrames/

.html

CLONE_LINK

http://www.chickest.udel.edu/Cogburn_CAP3_DB/UDEST/

.html

LOCALISATION Localisation of the gene on Chicken Assembly

http://genome.ucsc.edu/cgi-bin/hgTracks?org=Chicken&db=galGal2&position=

&pix=620&hgsid=37661781&Submit=Submit

DNA concentration Overall Array Row Overall Array Column SubarrRow SubarrCol Row Column

1 pgp1c.pk001.i17 BI390360 putative FK506-binding protein [Gallus gallus] Gallus gallus mRNA for putative FK506-binding protein (FKBP25 gene) Contig_13835.1 pgp1c/pgp1c.pk001.i17 chr5:55459886-55464886 60.8 1 1 1 1 1 1 2 pgp1c.pk002.a15 BI389781 No Hits Found No Hits Found pgp1c/pgp1c.pk002.a15 chr19:197813-202813 0.1 1 2 1 1 1 2 3 pgp1c.pk002.f23 BI389872 No Hits Found Homo sapiens genomic DNA, chromosome 11q clone:RP11-64D24, complete sequence Contig_16671.1 pgp1c/pgp1c.pk002.f23 chr24:4336858-4341858 98.7 1 3 1 1 1 3 4 pgp1c.pk002.l20 BI390388 Tnf receptor-associated factor 2 [Mus musculus] Homo sapiens TNF receptor-associated factor 2 (TRAF2), transcript variant 2, mRNA pgp1c/pgp1c.pk002.l20 chr17:10311815-10316815 14.4 1 4 1 1 1 4 5 pgp1c.pk003.c11 BI390394 H2A histone family, member Z; H2AZ histone [Homo sapiens] Bovine mRNA for histone H2A.Z Contig_11784.2 pgp1c/pgp1c.pk003.c11 chrUn:145716420-145721420 19.1 1 5 1 1 1 5 6 pgp1c.pk003.h18 BI390179 unnamed protein product [Mus musculus] No Hits Found Contig_581.1 pgp1c/pgp1c.pk003.h18 chr3:5840848-5845848 27.3 1 6 1 1 1 6 7 pgp1c.pk001.i7 BI390361 zinc-finger helicase [Homo sapiens] Homo sapiens chromodomain helicase DNA binding protein 3 (CHD3), mRNA Contig_12844.1 pgp1c/pgp1c.pk001.i7 chr21:570529-575529 107.5 1 7 1 1 1 7 8 pgp1c.pk002.a18 BI389784 hypothetical protein MGC10963 [Homo sapiens] Homo sapiens Chromosome 22q11.2 PAC Clone p_n5 In BCRL2-GGT Region, complete sequence Contig_1402.2 pgp1c/pgp1c.pk002.a18 chrUn:40415515-40420515 8.5 1 8 1 1 1 8 9 pgp1c.pk002.f3 BI389874 No Hits Found No Hits Found pgp1c/pgp1c.pk002.f3 61.5 1 9 1 1 1 9 10 pgp1c.pk002.l22 BI389975 No Hits Found Homo sapiens clone 23969 mRNA sequence Contig_13197.1 pgp1c/pgp1c.pk002.l22 chr1:49812094-49817094 147.9 1 10 1 1 1 10 11 pgp1c.pk003.c14 BI390395 reticulocalbin 2 [Rattus norvegicus] Homo sapiens reticulocalbin 2, EF-hand calcium binding domain(RCN2), mRNA Contig_4776.1 pgp1c/pgp1c.pk003.c14 chr10:3993128-3998128 24.2 1 11 1 1 1 11 12 pgp1c.pk003.h23 BI390185 S-adenosylhomocysteine hydrolase-like 1; S-adenosyl homocysteinehydrolase homolog [Homo sapiens] Homo sapiens S-adenosylhomocysteine hydrolase-like 1 (AHCYL1), mRNA Contig_11827.3 pgp1c/pgp1c.pk003.h23 chr26:4915-9915 25.2 1 12 1 1 1 12 13 pgp1c.pk001.j14 BI389685 KIAA1068 protein [Homo sapiens] Homo sapiens, Similar to KIAA1068 protein, clone MGC:14963 IMAGE:4300217, mRNA, complete cds Contig_4440.1 pgp1c/pgp1c.pk001.j14 chrUn:149829188-149834188 162.4 1 13 1 1 1 13 14 pgp1c.pk002.a20 BI389786 No Hits Found No Hits Found Contig_23259.1 pgp1c/pgp1c.pk002.a20 chr1:164961895-164966895 34.9 1 14 1 1 1 14 15 pgp1c.pk002.f7 BI389876 No Hits Found Homo sapiens 3 BAC RP11-305O4 (Roswell Park Cancer Institute Human BAC Library) complete sequence Contig_1352.2 pgp1c/pgp1c.pk002.f7 chr4:60295673-60300673 42.9 1 15 1 1 1 15 16 pgp1c.pk001.j21 BI390429 DIHYDROPYRIMIDINASE RELATED PROTEIN-2 (DRP-2) (COLLAPSIN RESPONSE MEDIATOR PROTEIN CRMP-62) Gallus gallus collapsin response mediator protein CRMP-62 mRNA, complete cds Contig_13062.1 pgp1c/pgp1c.pk001.j21 chr22:484701-489701 102.7 1 16 1 2 1 1 17 pgp1c.pk002.a24 BI389790 hypothetical protein [Homo sapiens] Homo sapiens, Similar to hypothetical gene supported by AL050367; AK022946, clone MGC:34829 IMAGE:52 pgp1c/pgp1c.pk002.a24 4.8 1 17 1 2 1 2 18 pgp1c.pk002.g18 BI389884 No Hits Found No Hits Found Contig_2477.2 pgp1c/pgp1c.pk002.g18 chr4:69486522-69491522 75 1 18 1 2 1 3 19 pgp1c.pk002.m23 CD218760 elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3,yeast)-like 1 [Homo sapiens] Homo sapiens elongation of very long chain fatty acids (FEN1/Elo2,SUR4/Elo3, yeast)-like 1 (ELOVL1), Contig_11907.6 pgp1c/pgp1c.pk002.m23 chr8:19981028-19986028 24.7 1 19 1 2 1 4 20 pgp1c.pk003.c4 BI390094 No Hits Found No Hits Found Contig_7042.1 pgp1c/pgp1c.pk003.c4 chr7:28894362-28899362 2.2 1 20 1 2 1 5

Chicken pituitary gland, embryonic day 10, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 10 Gallus gallus Chicken embryonic pituitary gland, embryonic day 10

Allen's Hatchery (Seaford, Delaware)

Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 10. Pituitary glands from 16 embryonic day 10 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.

total RNA

Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) and was amplifed using a modification of the Eberwine Procedure (Phillips J, Eberwine JH 1996 METHODS: A Companion to Methods in Enzymology 10: 283-288). Briefly, 500 ng was reverse-transcribed using SuperScript II (Invitrogen, Carlsbad, CA) and an oligo(dT) primer containing a T7 promoter site (5'-GGCCAGTGAATTGTAATATCGACTCACTATAGGGAGGCGGT24-3'; Affymetrix, Santa Clara, CA). Following second strand synthesis and purification, double-stranded cDNA was used as a template for in vitro transcription using the T7 MEGAscript kit (Ambion, Austin, TX) and the resulting amplified antisense RNA was quantified with the Ribogreen RNA Quantitation Kit (Invitrogen, Carlsbad, CA).

Cy3

1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion), and Cy3-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA. Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences).

Reference pool of chicken embryonic pituitary gland amplified RNA, embryonic days 10, 12, 14, and 17 Gallus gallus Chicken embryonic pituitary amplified antisense RNA, pooled from all replicates (n=4) on each of embryonic days 10, 12, 14, and 17 to be used as a reference sample (16 samples total) total RNA

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

1 microgram amplified antisense RNA (equivalent to 1 microgram mRNA) from the pool was converted to cDNA using random primers with the Amino Allyl cDNA Labeling Kit (Ambion) and Cy5-monoreactive NHS esters (Amersham Biosciences, Piscataway, NJ) were coupled to the cDNA. Labeled cDNA was purified from unicorporated dye using CyScribe GFX Purification Kit (Amersham Biosciences) and a pool was made of all Cy5-labeled cDNA to be split among the 16 slides in the experiment.

The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 10 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences). Slides were washed in increasing stringency using salt sodium citrate.

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 10, replicate 1

The two images from each slide were processed with Spotfinder version 2.2.4 (The Institute for Genomic Research, Rockville, MD) using the following settings: Otsu thresholding algorithm (minimum spot size 3 and maximum spot size 25); keep flagged values; keep raw data; and quality control filter set so 50% cutoff equals background plus 1 standard deviation. Data were normalized using Microarray Data Analysis System (MIDAS) version 2.18 (The Institute for Genomic Research). In MIDAS, channel A and B flags and channel A and B background checking were used, and the signal-to-noise threshold was set at 3.0. Data from the Cy3 channel were first Lowess (LocFit) normalized by pin (block) using a smoothing parameter of 0.33 with Cy5 as the reference and then sujected to standard deviation regularization first by pin (block) then by slide with Cy5 as the reference. A cross file cutoff of 25% was used, so that at least 4 of the 16 slides for a given spot had to pass quality control checks. The data from each spot on each slide were then expressed as log2-ratio, or log2(normalized Cy3/raw Cy5), which is given in the data table below. Log2-ratios for the spots were statistically analyzed by one-way analysis of variance using Statistical Analysis Systems version 8.02 (SAS Institute, Cary, NC) to identify cDNAs that were differentially expressed on at least one of the developmental ages (n = 4; P < 0.05), and a fold-change of > 1.6 was used as a filter for false positives.

Sample1_Cy3.tif

Sample1_Cy5.tif

ID_REF ID in platform VALUE log2(normalized Cy3/raw Cy5) CH1_Normalized Cy3 normalized intensity CH2_RAW Cy5 raw intensity CH1_RAW Cy3 raw intensity CH1_Flag Cy 3 flags; B (0-50 non-saturated pixels in spot) and C (> 50 non-saturated pixels in spot) denote satisfactory values; A (0 non-saturated pixels in spot), X (spot rejected due to shape and intensity relative to background), Y (background higher than spot intensity), and Z (spot not detected) denote unsatisfactory values CH2_Flag Cy 5 flags; B (0-50 non-saturated pixels in spot) and C (> 50 non-saturated pixels in spot) denote satisfactory values; A (0 non-saturated pixels in spot), X (spot rejected due to shape and intensity relative to background), Y (background higher than spot intensity), and Z (spot not detected) denote unsatisfactory values Area Spot area in pixels Sat_Factor saturation factor QCscore average quality control score for both channels (Cy3 and Cy5) CH1_QC quality control score for Cy3 CH2_QC quality control score for Cy5 CH1_Bkgd background value for Cy3 CH2_Bkgd background value for Cy5

1 0.046191544 3736385 3618650 4735775 C C 155 1 0.9805 0.9805 0.9805 80135 45105 2 0.104225332 339189 315549 596951 C C 124 1 0.9939 0.996 0.9919 61752 35588 3 -0.290018217 146356 178943 247150 C C 135 1 0.766 0.7763 0.7556 66420 37260 4 -0.187977443 78712 89666 146022 C C 79 1 0.943 0.9554 0.9306 37525 21725 5 0.446354383 1969655 1445520 3140601 C C 139 1 0.945 0.9556 0.9344 70890 43090 6 -0.136371432 123314 135539 222774 C C 109 1 0.9447 0.9589 0.9305 49704 30629 7 0.013726482 225781 223643 407608 C C 135 1 0.8225 0.8287 0.8162 63990 44145 8 -0.092475733 412035 439311 651883 C C 129 1 0.9902 0.9961 0.9844 62178 43602 9 -1.086200351 879015 1866273 879745 C C 124 1 0.9919 0.9878 0.996 58900 39060 10 0.365373325 742996 576764 1354731 C C 145 1 0.9786 0.9873 0.97 78445 49300 11 0.110372985 1403964 1300560 2102237 C C 144 1 0.974 0.9792 0.9688 76752 49824 12 -0.102713594 408883 439055 644901 C C 162 1 0.7467 0.7503 0.7431 82944 56538 13 -0.075835916 694755 732252 1075937 C C 126 1 0.986 0.984 0.988 64764 47628 14 0.055189195 463687 446284 765889 C C 101 1 0.9353 0.945 0.9257 52419 37572 15 0.242378876 931492 787437 1569716 C C 97 1 0.9285 0.9435 0.9136 47336 35211 16 0.328818062 420202 334560 737959 C C 72 1 0.9018 0.9116 0.8921 34488 21672 17 0.086146018 116969 110189 230190 C C 124 1 0.7646 0.7811 0.7482 59892 33852 18 0.142219108 335401 303915 585090 C C 132 1 0.9866 0.9962 0.977 62040 35244 19 0.101417587 1337677 1246871 2016575 C C 138 1 0.9927 0.9964 0.9891 65688 35190 20 0.363258551 82343 64014 176936 C C 113 1 0.2819 0.3092 0.2547 50624 27346

Chicken pituitary gland, embryonic day 10, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 10 Gallus gallus Chicken embryonic pituitary gland, embryonic day 10

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 10, replicate 2

Sample2_Cy3.tif

Sample2_Cy5.tif

1 0.211716478 3500911 3023069 3956697 C C 152 1 0.9372 0.9455 0.929 57000 31160 2 0.176358765 264152 233757 371313 C C 111 1 0.9189 0.9297 0.9081 41070 23865 3 -0.406712526 91939 121880 117679 C C 124 1 0.5004 0.4971 0.5038 46252 22568 4 0.032313764 86143 84235 128447 C C 84 1 0.8934 0.9167 0.8702 28812 15036 5 0.56802547 1367766 922612 1886166 C C 126 1 0.9758 0.992 0.9595 47376 26082 6 -0.012024119 75275 75905 113210 C C 101 1 0.8902 0.9144 0.866 33027 18584 7 0.137146716 181928 165430 260304 C C 117 1 0.8497 0.8611 0.8384 39195 21177 8 -0.006136519 348616 350102 451248 C C 115 1 0.9846 0.9956 0.9736 39675 22080 9 -1.082408745 655736 1388566 610341 C C 115 1 0.9779 0.9601 0.9956 40365 22885 10 0.397670844 391537 297209 564849 C C 139 1 0.8612 0.8758 0.8465 46148 26549 11 0.115503237 1067368 985245 1329572 C C 150 1 0.9849 0.9899 0.9798 50700 29250 12 -0.068670088 301993 316715 390472 C C 151 1 0.8031 0.8045 0.8017 49075 26727 13 0.156954222 476944 427779 636552 C C 118 1 0.9742 0.9786 0.9699 37170 19470 14 0.133251884 352685 321569 475796 C C 105 1 0.946 0.9533 0.9387 32655 18585 15 0.162502931 655143 585353 875848 C C 95 1 0.976 0.9841 0.9679 30020 17195 16 0.289627784 250051 204570 375175 C C 71 1 0.9323 0.9428 0.9218 24495 13419 17 0.116158803 103918 95879 157958 C C 118 1 0.6011 0.6066 0.5955 39530 18644 18 0.036872492 215501 210063 317976 C C 148 1 0.8219 0.8335 0.8103 51948 26936 19 0.364405594 1063334 825986 1423061 C C 119 1 0.9916 0.9958 0.9873 40817 27370 20 0.396850605 83294 63263 133059 C C 128 1 0.2698 0.3006 0.239 47872 26368

Chicken pituitary gland, embryonic day 10, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 10 Gallus gallus Chicken embryonic pituitary gland, embryonic day 10

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 10, replicate 3

Sample3_Cy3.tif

Sample3_Cy5.tif

1 0.147750975 2791055 2519364 2348965 C C 148 1 0.983 0.983 0.983 61864 26344 2 0.046280418 252391 244423 278480 C C 107 1 0.9235 0.9235 0.9235 44619 20223 3 -0.343894113 76143 96639 82616 C C 105 1 0.4337 0.4302 0.4372 40740 19320 4 -0.176093946 94746 107046 104731 C C 78 1 0.9113 0.9022 0.9203 32136 13416 5 0.279658013 1354832 1116092 1418519 C C 125 1 0.9879 0.996 0.9798 52625 23250 6 -0.172078017 63759 71836 80967 C C 86 1 0.5503 0.5573 0.5432 34744 14878 7 -0.067080979 157937 165454 166610 C C 115 1 0.717 0.7121 0.7218 46230 20240 8 -0.20705298 242594 280033 234649 C C 86 1 0.9457 0.9457 0.9457 35174 15480 9 -1.152180055 391708 870569 200101 C C 69 1 0.7759 0.7701 0.7817 29532 13524 10 0.352719847 404069 316429 470108 C C 132 1 0.961 0.961 0.961 52272 23496 11 0.241977377 875216 740070 932923 C C 131 1 0.9923 0.9962 0.9885 52269 19126 12 0.134957053 291401 265378 325719 C C 136 1 0.9062 0.9079 0.9045 51408 25024 13 0.06730317 447547 427148 435437 C C 88 1 0.9857 0.977 0.9943 33968 14872 14 0.186308457 260928 229317 308723 C C 90 1 0.9888 0.9944 0.9832 35010 15120 15 0.21418836 598388 515829 614292 C C 81 1 0.9876 0.9813 0.9938 29808 15471 16 0.385099598 360753 276238 361493 C C 73 1 0.9744 0.971 0.9778 26572 13505 17 0.158076286 98236 88041 110632 C C 102 1 0.7537 0.7615 0.7458 37944 18666 18 0.251119661 220768 185499 222204 C C 117 1 0.9128 0.9087 0.9169 42471 20007 19 0.089846337 907694 852890 687402 C C 114 1 0.986 0.9838 0.9883 42636 21888 20 -0.071890618 60967 64082 75332 C C 105 1 0.3051 0.3061 0.3042 38430 20055

Chicken pituitary gland, embryonic day 10, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 10 Gallus gallus Chicken embryonic pituitary gland, embryonic day 10

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 10, replicate 4

Sample4_Cy3.tif

Sample4_Cy5.tif

1 0.284567229 1922160 1578070 2131756 C C 178 1 0.7196 0.7263 0.713 42542 23318 2 0.907963537 108450 57797 188863 C C 107 1 0.3848 0.4038 0.3658 24503 11663 3 -0.234815728 42188 49645 57108 C C 124 1 0.3853 0.3938 0.3768 25172 11284 4 0.362249765 36028 28028 56906 C C 80 1 0.4869 0.5203 0.4536 14240 7520 5 0.590050632 321535 213602 463040 C C 108 1 0.9201 0.9455 0.8946 20628 11232 6 0.417495957 33282 24919 53495 C C 87 1 0.412 0.4542 0.3697 16008 7395 7 0.205277354 54732 47473 81598 C C 124 1 0.249 0.2651 0.2329 22692 11532 8 -0.049605747 83843 86776 116294 C C 133 1 0.454 0.4531 0.4549 24738 11837 9 -0.538894204 363162 527623 373548 C C 139 1 0.7692 0.7557 0.7827 27939 15290 10 0.23769101 196480 166635 277944 C C 149 1 0.7631 0.7811 0.745 28608 18774 11 0.13341522 221297 201750 300538 C C 151 1 0.5149 0.5177 0.5121 30804 17969 12 0.024801372 128021 125839 177858 C C 148 1 0.423 0.4288 0.4173 27972 16724 13 -0.062253094 170722 178250 226441 C C 94 1 0.9536 0.9676 0.9397 15980 10152 14 -0.048460006 93500 96694 129662 C C 100 1 0.6586 0.6718 0.6455 18100 10500 15 -0.003053272 118474 118725 164206 C C 101 1 0.8565 0.8613 0.8517 17877 10100 16 0.283956513 41424 34023 65534 C C 82 1 0.7891 0.817 0.7613 13530 7626 17 -0.10379634 23352 25094 33757 C C 90 1 0.0883 0.0959 0.0806 15660 8280 18 -0.11233216 81211 87787 102253 C C 120 1 0.2002 0.2036 0.1968 23280 13680 19 -0.094687607 862132 920614 940921 C C 176 1 0.9653 0.9624 0.9682 32736 21648 20 -0.025375625 26825 27301 39490 C C 99 1 0.0747 0.0817 0.0676 18909 11088

Chicken pituitary gland, embryonic day 12, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 12 Gallus gallus Chicken embryonic pituitary gland, embryonic day 12

Allen's Hatchery (Seaford, Delaware)

Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 12. Pituitary glands from 8 embryonic day 12 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 12 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences). Slides were washed in increasing stringency using salt sodium citrate.

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 12, replicate 1

Sample5_Cy3.tif

Sample5_Cy5.tif

1 0.355193938 5152545 4028077 4988036 C C 131 1 0.9827 0.9846 0.9807 55806 33012 2 -0.098801823 323149 346055 384108 C C 112 1 0.9317 0.9274 0.9359 46256 26320 3 -0.415548943 129030 172101 158350 C C 120 1 0.8595 0.8481 0.8709 46200 25320 4 0.095967374 108740 101742 144255 C C 84 1 0.88 0.8828 0.8772 34608 19992 5 0.390191172 2079136 1586440 2201631 C C 135 1 0.9447 0.9537 0.9356 53190 28890 6 0.240805849 150435 127309 193036 C C 112 1 0.7661 0.7679 0.7643 44576 24864 7 0.129616784 214662 196217 261815 C C 112 1 0.9338 0.9402 0.9274 44464 23744 8 -0.206374214 412765 476242 486396 C C 111 1 0.9841 0.9818 0.9864 41403 25197 9 -1.025163019 986293 2007293 1027079 C C 102 1 0.9446 0.9326 0.9566 41106 26316 10 0.17528449 590645 523071 714889 C C 134 1 0.9207 0.9207 0.9207 51858 32562 11 0.161926733 1349635 1206345 1526419 C C 134 1 0.9594 0.9631 0.9558 55342 30552 12 0.174258121 552854 489952 668559 C C 150 1 0.9809 0.9894 0.9725 58650 37050 13 0.255203572 946703 793213 1138340 C C 109 1 0.9838 0.9815 0.9861 45453 26814 14 0.267705889 525305 436339 637686 C C 102 1 0.9306 0.9306 0.9306 40392 25092 15 0.409731211 1048810 789506 1262309 C C 89 1 0.983 0.9773 0.9887 34710 23318 16 -0.205538991 391746 451729 482415 C C 87 1 0.9826 0.9826 0.9826 33930 20880 17 -0.151643414 115533 128338 146716 C C 98 1 0.7276 0.7276 0.7276 36750 25284 18 0.405625031 443558 334846 513495 C C 137 1 0.9653 0.9635 0.9671 55211 34250 19 0.55077937 2109512 1440061 2206286 C C 107 1 0.9904 0.9904 0.9904 46010 29746 20 0.540965898 111203 76431 133015 C C 123 1 0.2887 0.3161 0.2613 48585 31980

Chicken pituitary gland, embryonic day 12, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 12 Gallus gallus Chicken embryonic pituitary gland, embryonic day 12

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 12, replicate 2

Sample6_Cy3.tif

Sample6_Cy5.tif

1 0.094763551 1918417 1796455 3013874 C C 128 1 0.9822 0.9961 0.9682 56448 27008 2 -0.101314545 83051 89093 181679 C C 97 1 0.6509 0.667 0.6349 42098 21922 3 -0.091489844 47350 50450 103245 C C 114 1 0.4144 0.4651 0.3636 46284 25308 4 -0.349507295 42849 54595 96890 C C 77 1 0.6327 0.6464 0.6189 31493 16093 5 0.157584765 464449 416390 843546 C C 119 1 0.9658 0.9828 0.9489 47719 27727 6 0.177277502 45983 40666 96186 C C 90 1 0.7225 0.805 0.64 35820 19080 7 -0.065863215 73473 76905 159996 C C 108 1 0.6386 0.6683 0.6089 41796 22356 8 -0.063545092 139039 145300 293764 C C 99 1 0.8826 0.8942 0.8711 41877 21879 9 -1.236443775 314024 739894 682113 C C 115 1 0.9891 0.9869 0.9913 50600 28635 10 -0.062643379 146876 153394 309284 C C 126 1 0.8472 0.8686 0.8258 55062 34272 11 0.127778107 403834 369605 747681 C C 132 1 0.9789 0.9924 0.9653 55968 31812 12 0.087722882 167494 157613 344045 C C 133 1 0.8623 0.8811 0.8436 57190 35378 13 -0.021895602 237827 241464 481387 C C 97 1 0.907 0.9168 0.8973 43359 27160 14 0.187804091 157514 138288 320871 C C 99 1 0.9139 0.931 0.8968 41679 26532 15 0.385667026 270502 207049 519851 C C 86 1 0.9733 0.9942 0.9524 37152 24510 16 0.052910169 94390 90991 207501 C C 67 1 0.8951 0.9127 0.8774 24321 12462 17 0.38505171 57042 43680 116107 C C 112 1 0.4988 0.5811 0.4164 40768 21840 18 0.179242854 111004 98035 235734 C C 122 1 0.7764 0.7971 0.7558 45140 24156 19 0.640325669 730945 468951 1256832 C C 106 1 0.9506 0.9622 0.939 38160 21200 20 0.371258285 56961 44037 116335 C X 121 1 0.2801 0.3372 0.2229 41987 23111

Chicken pituitary gland, embryonic day 12, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 12 Gallus gallus Chicken embryonic pituitary gland, embryonic day 12

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 12, replicate 3

Sample7_Cy3.tif

Sample7_Cy5.tif

1 -0.315278101 35009 43560 56683 C C 57 1 0.6947 0.7092 0.6802 17328 7182 2 -0.377194091 443424 575925 399774 C C 105 1 0.7924 0.7765 0.8082 35175 16905 3 0.404958133 45738 34544 74986 C X 127 1 0.1381 0.1648 0.1115 41529 19050 4 -0.285345998 163839 199671 175317 C C 82 1 0.9189 0.9042 0.9335 26568 13612 5 -0.323046579 109854 137424 128026 C C 77 1 0.8955 0.8863 0.9046 25102 11165 6 -0.141455519 229272 252891 231570 C C 90 1 0.8818 0.8767 0.8868 29970 14580 7 -0.131726121 941145 1031122 802186 C C 113 1 0.9866 0.9776 0.9956 35143 20001 8 -0.25320597 1462304 1742851 1178392 C C 88 1 0.9492 0.9351 0.9632 31240 18392 9 -0.134076634 355395 390007 339349 C C 131 1 0.8864 0.8777 0.8951 42051 22139 10 -0.157071768 330642 368673 318124 C C 115 1 0.9292 0.9188 0.9396 39905 20355 11 0.120471224 35088 32277 59953 C X 114 1 0.1071 0.1257 0.0884 34200 18924 12 0.104340122 823008 765587 715221 C C 124 1 0.9939 0.9919 0.996 43400 23932 13 -0.197002664 36818 42205 59623 C C 88 1 0.2343 0.2538 0.2148 30536 16720 14 0.105506889 256687 238585 259749 C C 109 1 0.8984 0.8942 0.9025 39349 21146 15 0.184850003 267322 235174 270568 C C 99 1 0.9075 0.9005 0.9146 37026 21483 16 0.166882617 57436 51162 73326 C C 116 1 0.1528 0.1679 0.1378 42804 25984 17 0.246170521 185767 156626 168024 C C 116 1 0.6372 0.6415 0.633 40948 26796 18 0.060539712 56309 53995 72741 C C 105 1 0.2378 0.2523 0.2234 36120 23100 19 -0.248254304 655630 778737 554747 C C 106 1 0.9814 0.9791 0.9838 40810 23638 20 -0.092216153 40996 43702 59605 C C 96 1 0.1532 0.1611 0.1453 33120 17088

Chicken pituitary gland, embryonic day 12, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 12 Gallus gallus Chicken embryonic pituitary gland, embryonic day 12

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 12, replicate 4

Sample8_Cy3.tif

Sample8_Cy5.tif

1 0 0 0 Z Z 999 0 0 0 0 0 0 2 0 0 0 Z Z 999 0 0 0 0 0 0 3 0 0 0 Z Z 999 0 0 0 0 0 0 4 0 0 0 Z Z 999 0 0 0 0 0 0 5 0 0 0 Z Z 999 0 0 0 0 0 0 6 0 0 0 Z Z 999 0 0 0 0 0 0 7 0 0 0 Z Z 999 0 0 0 0 0 0 8 0 0 0 Z Z 999 0 0 0 0 0 0 9 0 0 0 Z Z 999 0 0 0 0 0 0 10 0 0 0 Z Z 999 0 0 0 0 0 0 11 0 0 0 Z Z 999 0 0 0 0 0 0 12 0 0 0 Z Z 999 0 0 0 0 0 0 13 0 0 0 Z Z 999 0 0 0 0 0 0 14 0 0 0 Z Z 999 0 0 0 0 0 0 15 0 0 0 Z Z 999 0 0 0 0 0 0 16 -0.073547535 11625 12233 28448 C X 79 1 0.0604 0.0752 0.0457 12561 7031 17 0 0 0 Z Z 999 0 0 0 0 0 0 18 0 0 0 Z Z 999 0 0 0 0 0 0 19 -0.198321832 126884 145582 284248 C C 138 1 0.731 0.7337 0.7283 35880 18216 20 0 0 0 Z Z 999 0 0 0 0 0 0

Chicken pituitary gland, embryonic day 14, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 14 Gallus gallus Chicken embryonic pituitary gland, embryonic day 14

Allen's Hatchery (Seaford, Delaware)

Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 14. Pituitary glands from 4 embryonic day 14 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 14 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences). Slides were washed in increasing stringency using salt sodium citrate.

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 14, replicate 1

Sample9_Cy3.tif

Sample9_Cy5.tif

1 0.57481993 2514293 1688021 2898991 C C 144 1 0.9753 0.986 0.9647 54144 24624 2 -0.028749545 86399 88138 138347 C C 111 1 0.6856 0.6986 0.6725 36519 17649 3 0.474118527 64607 46511 119774 C C 123 1 0.4434 0.4811 0.4056 40959 18327 4 -0.021860414 55345 56190 97157 C C 81 1 0.7847 0.8137 0.7556 27459 12555 5 -0.043168693 412123 424641 544246 C C 149 1 0.9779 0.9797 0.9762 52746 24883 6 0.341456648 47211 37261 91743 C C 103 1 0.496 0.5697 0.4222 34505 17407 7 -0.064270694 89823 93915 141799 C C 127 1 0.5601 0.5819 0.5384 41529 24638 8 -0.184190332 141424 160683 208817 C C 120 1 0.8652 0.8746 0.8558 39960 20040 9 -0.272759854 571314 690214 702804 C C 128 1 0.9862 0.9803 0.9922 43264 24576 10 -0.026336592 79304 80765 129302 C C 102 1 0.5637 0.5833 0.5441 34476 18054 11 -0.03924698 212312 218167 311162 C C 98 1 0.5568 0.5629 0.5508 34790 19992 12 0.099200874 205583 191922 306288 C C 150 1 0.7799 0.7826 0.7771 50700 27000 13 0.181220809 260319 229590 386341 C C 113 1 0.982 0.9956 0.9685 40454 20792 14 0.219686294 177008 152006 271938 C C 106 1 0.9413 0.9437 0.939 40068 20140 15 0.587890994 351856 234095 527895 C C 92 1 0.9779 0.9946 0.9612 32476 19228 16 -0.630710091 96975 150149 130038 C C 97 1 0.8521 0.8379 0.8663 29197 16393 17 0.149976134 50499 45513 81800 C C 102 1 0.3477 0.3783 0.3172 31212 17850 18 0.384815913 111484 85383 172991 C C 111 1 0.9009 0.9339 0.8679 36852 19314 19 0.428708016 356416 264791 517065 C C 80 1 0.5961 0.5981 0.5941 28880 15920 20 0.403291043 58306 44087 97185 C C 112 1 0.2088 0.2379 0.1798 40656 20720

Chicken pituitary gland, embryonic day 14, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 14 Gallus gallus Chicken embryonic pituitary gland, embryonic day 14

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 14, replicate 2

Sample10_Cy3.tif

Sample10_Cy5.tif

1 -0.37799399 2467666 3206815 3907510 C C 160 1 0.8661 0.8632 0.8689 73280 31040 2 0.096739464 103568 96851 195124 C C 88 1 0.5632 0.5988 0.5277 41624 20680 3 0.188007826 104720 91925 194683 C C 118 1 0.6396 0.6555 0.6236 51684 21476 4 0.03156101 48570 47519 100690 C C 71 1 0.4566 0.4659 0.4473 30459 13277 5 0.140010276 768646 697556 1209743 C C 103 1 0.9258 0.9281 0.9234 45114 19776 6 0.211721466 62186 53698 122369 C C 80 1 0.819 0.8356 0.8024 33920 14320 7 -0.161475459 63455 70970 130912 C C 79 1 0.5763 0.6004 0.5523 33022 15326 8 0.003060581 266612 266047 468137 C C 115 1 0.989 0.9956 0.9825 46575 23000 9 0.59257854 1435863 952202 2041961 C C 104 1 0.9098 0.9281 0.8914 45656 24128 10 -0.053318797 235835 244714 419678 C C 116 1 0.8637 0.8753 0.8522 48604 23664 11 0.422825372 791540 590459 1192282 C C 133 1 0.9506 0.9655 0.9358 54929 29925 12 0.018835052 261283 257894 457755 C C 147 1 0.7011 0.7062 0.6961 59094 31017 13 -0.295620017 324226 397959 592305 C C 98 1 0.9118 0.9191 0.9044 38808 19600 14 0.127498953 225400 206335 390945 C C 84 1 0.9558 0.9588 0.9528 32676 17220 15 0.160517318 423958 379317 707166 C C 79 1 0.9524 0.9554 0.9493 31837 16037 16 -0.427151439 95854 128883 193834 C C 60 1 0.9189 0.9311 0.9067 22500 11400 17 -0.002777554 76799 76947 146492 C C 117 1 0.7193 0.7394 0.6991 44694 23985 18 -0.169600691 166096 186816 310659 C C 131 1 0.9463 0.9519 0.9407 51745 27903 19 0.206247439 1158567 1004233 1771735 C C 135 1 0.9849 0.9942 0.9755 53595 31050 20 0.219205018 53426 45895 97716 C X 104 1 0.1563 0.1812 0.1314 42120 21528

Chicken pituitary gland, embryonic day 14, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 14 Gallus gallus Chicken embryonic pituitary gland, embryonic day 14

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 14, replicate 3

Sample11_Cy3.tif

Sample11_Cy5.tif

1 -0.667741475 378595 601430 372694 C C 122 1 0.9876 0.9793 0.9959 37942 23790 2 0 0 0 Z Z 999 0 0 0 0 0 0 3 0 0 0 Z Z 999 0 0 0 0 0 0 4 0 0 0 Z Z 999 0 0 0 0 0 0 5 0 0 0 Z Z 999 0 0 0 0 0 0 6 0 0 0 Z Z 999 0 0 0 0 0 0 7 0 0 0 Z Z 999 0 0 0 0 0 0 8 0 0 0 Z Z 999 0 0 0 0 0 0 9 -1.092826598 128503 274086 176553 C C 121 1 0.9425 0.9283 0.9566 37147 26741 10 0 0 0 Z Z 999 0 0 0 0 0 0 11 0 0 0 Z Z 999 0 0 0 0 0 0 12 0 0 0 Z Z 999 0 0 0 0 0 0 13 0 0 0 Z Z 999 0 0 0 0 0 0 14 0 0 0 Z Z 999 0 0 0 0 0 0 15 0 0 0 Z Z 999 0 0 0 0 0 0 16 0 0 0 Z Z 999 0 0 0 0 0 0 17 0 0 0 Z Z 999 0 0 0 0 0 0 18 0 0 0 Z Z 999 0 0 0 0 0 0 19 -0.618402242 296042 454476 299217 C C 123 1 0.9746 0.9623 0.9869 41451 36531 20 0 0 0 Z Z 999 0 0 0 0 0 0

Chicken pituitary gland, embryonic day 14, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 14 Gallus gallus Chicken embryonic pituitary gland, embryonic day 14

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 14, replicate 4

Sample12_Cy3.tif

Sample12_Cy5.tif

1 0.025957442 45145 44340 68219 C C 123 1 0.175 0.1909 0.1591 33210 19065 2 0.253745387 1549982 1299995 1453779 C C 113 1 0.9617 0.9574 0.966 40115 25877 3 0.07997052 253083 239436 281035 C C 128 1 0.8928 0.891 0.8946 42496 30080 4 -0.155819409 327888 365285 365090 C C 136 1 0.7686 0.7657 0.7714 50456 35224 5 -0.171209037 190172 214134 223842 C C 124 1 0.7075 0.7017 0.7134 41044 29264 6 -0.056389215 30557 31775 51195 C X 97 1 0.1039 0.1224 0.0855 28518 19594 7 -0.233449265 1811055 2129153 1794225 C C 126 1 0.8803 0.8767 0.8838 50022 33894 8 -0.05488192 101279 105206 127894 C C 145 1 0.3916 0.4007 0.3825 51910 36105 9 -0.216611012 28969 33662 49601 C X 100 1 0.0716 0.0782 0.065 31500 17000 10 0.841175678 2784751 1554416 2328925 C C 121 1 0.9712 0.9671 0.9753 43318 30976 11 -0.05405725 702532 729355 718422 C C 123 1 0.9869 0.9869 0.9869 44157 30873 12 0.048941941 153830 148699 180496 C C 112 1 0.7455 0.7472 0.7438 35728 24752 13 -0.148143256 132492 146820 161885 C C 108 1 0.7319 0.7301 0.7336 35964 25056 14 -0.210266322 123230 142565 153089 C C 128 1 0.6547 0.6547 0.6547 41728 29184 15 -0.291486285 46476 56882 70883 C C 116 1 0.1843 0.1934 0.1751 38280 25288 16 0 0 0 Z Z 999 0 0 0 0 0 0 17 0 0 0 Z Z 999 0 0 0 0 0 0 18 0 0 0 Z Z 999 0 0 0 0 0 0 19 0 0 0 Z Z 999 0 0 0 0 0 0 20 0 0 0 Z Z 999 0 0 0 0 0 0

Chicken pituitary gland, embryonic day 17, replicate 1 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 17 Gallus gallus Chicken embryonic pituitary gland, embryonic day 17

Allen's Hatchery (Seaford, Delaware)

Fertilized chicken eggs were placed in 37.5 C humidified incubator on embryonic day 0 and removed from the incubator on embryonic day 17. Pituitary glands from 2 embryonic day 17 embryos were pooled, immediately frozen in liquid nitrogen, and stored at -80 C until RNA extraction.

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray was hybridized overnight at 42 C with Cy3-labeled embryonic day 17 cDNA and an aliquot of the Cy5-labeled reference pool cDNA using microarray hybridization buffer (Amersham Biosciences). Slides were washed in increasing stringency using salt sodium citrate.

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 17, replicate 1

Sample13_Cy3.tif

Sample13_Cy5.tif

1 0.118337738 2432690 2241112 3457030 C C 159 1 0.9793 0.981 0.9777 60738 23850 2 -0.214720213 134242 155785 244273 C C 130 1 0.8364 0.8397 0.8331 45240 19110 3 0.63981967 105601 67774 209841 C C 136 1 0.7782 0.8365 0.7199 48008 20536 4 -0.27932337 44578 54101 92104 C C 80 1 0.8189 0.8411 0.7968 27760 10080 5 -0.06502682 487112 509570 797965 C C 134 1 0.9324 0.9416 0.9233 48508 20234 6 0.697696977 84672 52205 171921 C C 87 1 0.3319 0.3567 0.3071 32016 11745 7 -0.09084209 94366 100499 180711 C C 134 1 0.6591 0.6733 0.6449 45962 18358 8 -0.069859984 203407 213499 359140 C C 128 1 0.9527 0.9603 0.9451 45824 17792 9 0.958278493 1627225 837485 2571345 C C 137 1 0.9761 0.9853 0.967 52882 22331 10 0.199858598 224645 195584 399751 C C 141 1 0.8901 0.9032 0.877 50478 19317 11 0.22111463 444462 381305 751478 C C 139 1 0.966 0.9767 0.9553 51430 18209 12 0.22638531 214135 183037 383705 C C 151 1 0.7075 0.715 0.7001 51189 22197 13 0.213669037 329024 283731 573248 C C 109 1 0.979 0.9954 0.9626 37823 14933 14 0.223612213 141397 121095 264389 C C 95 1 0.9622 0.9841 0.9403 32300 13015 15 -0.050431987 258131 267314 450440 C C 88 1 0.9857 0.9943 0.977 30360 12408 16 -0.109305738 117801 127073 204914 C C 82 1 0.9783 0.9939 0.9627 27716 12054 17 -0.037011832 55952 57406 107112 C C 114 1 0.4203 0.4604 0.3802 38874 17784 18 0.54829742 161927 110730 272932 C C 142 1 0.6408 0.6588 0.6228 47286 24424 19 0.392737072 1035806 788956 1666444 C C 137 1 0.9635 0.9671 0.9599 50142 27537 20 0.303219538 48191 39056 93985 C X 115 1 0.1679 0.1971 0.1387 41285 19665

Chicken pituitary gland, embryonic day 17, replicate 2 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 17 Gallus gallus Chicken embryonic pituitary gland, embryonic day 17

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 17, replicate 2

Sample14_Cy3.tif

Sample14_Cy5.tif

1 0.060513451 1186351 1137619 2575551 C C 122 1 0.9918 0.9959 0.9876 53680 24766 2 -0.28060593 69514 84439 170416 C C 95 1 0.9017 0.9325 0.871 37525 17670 3 1.153717786 105047 47215 243189 C C 111 1 0.7671 0.8455 0.6888 45954 16872 4 0.028392337 47158 46239 117075 C C 71 1 0.8606 0.9011 0.8202 28684 11786 5 -0.114409508 358722 388328 775113 C C 120 1 0.9782 0.9887 0.9677 47160 21120 6 0.200777521 41095 35756 102773 C C 92 1 0.3826 0.4546 0.3105 35880 16928 7 -0.032016112 63280 64700 154801 C C 106 1 0.5745 0.5998 0.5491 42188 16430 8 0.138817362 169071 153561 382499 C C 112 1 0.9842 0.9955 0.9728 44016 20384 9 1.076831025 1025703 486254 2098703 C C 105 1 0.7561 0.7617 0.7506 43995 19005 10 -0.026641018 156779 159701 358107 C C 132 1 0.8573 0.8708 0.8438 54648 24024 11 0.108511372 351444 325980 757505 C C 124 1 0.9898 0.996 0.9837 49972 19220 12 0.218317125 158019 135828 362816 C C 127 1 0.8087 0.8168 0.8005 48387 22733 13 0.092510794 163369 153222 371442 C C 91 1 0.9805 0.9945 0.9665 33579 15470 14 -0.075716337 102943 108490 251553 C C 94 1 0.9811 0.9947 0.9676 38634 15792 15 -0.206395893 180173 207884 404353 C C 85 1 0.9851 0.9941 0.9762 33405 13345 16 -0.309354686 95052 117784 217492 C C 77 1 0.8541 0.8627 0.8455 28952 12012 17 0.274364665 47579 39339 107139 C C 98 1 0.4626 0.5258 0.3995 36652 16856 18 0.347487353 102874 80854 220243 C C 124 1 0.6736 0.7019 0.6454 45384 18848 19 0.420934687 452613 338075 949570 C C 115 1 0.8513 0.8532 0.8494 40250 18055 20 0.256915101 48558 40637 109561 C X 120 1 0.2719 0.3264 0.2174 43800 19800

Chicken pituitary gland, embryonic day 17, replicate 3 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 17 Gallus gallus Chicken embryonic pituitary gland, embryonic day 17

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 17, replicate 3

Sample15_Cy3.tif

Sample15_Cy5.tif

1 -0.072507158 995625 1046942 942901 C C 131 1 0.9631 0.9611 0.965 47815 21222 2 -0.820072138 51035 90102 65574 C C 88 1 0.7648 0.7373 0.7923 31064 10472 3 0.435053248 50128 37078 90748 C C 103 1 0.5046 0.5531 0.4561 34917 14420 4 0.114116538 28349 26193 61486 C X 109 1 0.15 0.1849 0.1151 32046 13625 5 -0.088841917 420098 446781 414881 C C 128 1 0.9682 0.9642 0.9723 39040 15744 6 -0.041182577 28387 29209 58724 C C 84 1 0.2325 0.2594 0.2056 28140 9240 7 -0.06739553 49411 51774 78353 C C 100 1 0.4678 0.5038 0.4318 32100 11000 8 -0.325636095 129940 162843 150066 C C 100 1 0.8757 0.8686 0.8827 35300 11500 9 0.970300904 1020953 521094 1158494 C C 95 1 0.9813 0.9947 0.9679 33345 13965 10 -0.032690045 127718 130645 159337 C C 108 1 0.8075 0.8035 0.8114 35532 12852 11 0.004684105 265617 264756 285065 C C 119 1 0.966 0.9617 0.9702 36771 13804 12 0.022015836 101754 100213 135327 C C 113 1 0.5011 0.5048 0.4974 35821 13786 13 0.044980217 149722 145126 181513 C C 86 1 0.9645 0.9584 0.9705 27004 11782 14 -0.08642123 90632 96227 119821 C C 87 1 0.9526 0.9613 0.9438 26970 11310 15 -0.35985622 190079 243928 197791 C C 80 1 0.9434 0.934 0.9527 26560 9600 16 -0.601063711 82806 125603 91570 C C 64 1 0.8965 0.8856 0.9075 20608 7936 17 -0.121364395 42854 46615 65575 C C 107 1 0.3993 0.4224 0.3763 32956 14231 18 0.26527586 88634 73747 113941 C C 99 1 0.5172 0.527 0.5074 32472 11088 19 0.221752234 313925 269198 338310 C C 98 1 0.9166 0.9287 0.9044 29008 11760 20 0.291332257 29521 24123 60149 C X 101 1 0.1035 0.126 0.0809 29896 12726

Chicken pituitary gland, embryonic day 17, replicate 4 vs. pituitary reference pool (embryonic days 10, 12, 14, 17)

Chicken embryonic pituitary gland, embryonic day 17 Gallus gallus Chicken embryonic pituitary gland, embryonic day 17

Allen's Hatchery (Seaford, Delaware)

total RNA

Cy3

Extraction and amplification was conducted as described for channel 1 for each of the 16 samples used in the study, and a pool was made of 2 micrograms from each sample.

Cy5

The microarray slides were scanned using a 418 confocal laser scanner (Affymetrix) at 550 nM for Cy3 and 649 nM for Cy5 to generate two TIFF images for each slide.

Chicken embryonic pituitary gland, embryonic day 17, replicate 4

Sample16_Cy3.tif

Sample16_Cy5.tif

1 0.227948649 3062663 2615049 2230697 C C 155 1 0.9821 0.9805 0.9837 60295 33635 2 -0.202732892 214858 247275 193562 C C 116 1 0.8973 0.8853 0.9094 47560 21576 3 1.14840755 221924 100115 215091 C C 123 1 0.8327 0.8488 0.8166 46002 25707 4 -0.357862933 87697 112386 90591 C C 84 1 0.7927 0.7799 0.8054 31752 17556 5 -0.399659922 726492 958386 551115 C C 116 1 0.9477 0.9306 0.9648 44428 25056 6 0.232633399 80419 68443 92960 C C 96 1 0.5881 0.607 0.5691 34848 17568 7 -0.08243205 167700 177561 154900 C C 127 1 0.7229 0.7199 0.7259 43688 27305 8 -0.021504959 420236 426547 338817 C C 122 1 0.9834 0.9751 0.9918 41358 23302 9 0.872564411 2744149 1498786 2072565 C C 123 1 0.9795 0.9836 0.9753 44403 27675 10 0.088592338 342847 322427 291075 C C 138 1 0.8285 0.8206 0.8364 49542 25944 11 0.051042576 910376 878730 694821 C C 147 1 0.9846 0.9828 0.9863 50127 31752 12 0.228043875 384862 328592 323348 C C 152 1 0.6797 0.6808 0.6785 53048 30248 13 0.1355796 394544 359155 326741 C C 96 1 0.9047 0.9047 0.9047 31584 18528 14 -0.03504333 268062 274653 234997 C C 105 1 0.9252 0.9228 0.9275 37380 19950 15 -0.440416962 461576 626357 359593 C C 94 1 0.9646 0.9453 0.9839 32806 18988 16 -0.215417407 281328 326633 219805 C C 91 1 0.9692 0.9496 0.9889 29757 19383 17 -0.031125744 111788 114226 105694 C C 117 1 0.7357 0.7391 0.7323 39897 24687 18 0.187324064 259652 228035 208249 C C 144 1 0.6826 0.6764 0.6888 49392 27792 19 0.561758451 1307924 886087 979697 C C 125 0.984 0.9898 0.9918 0.9877 42927 30996 20 0.515368871 76172 53291 84577 C C 117 1 0.2668 0.2934 0.2401 39195 23751

Global gene expression profiling during pituitary thyrotroph, somatotroph, and lactotroph differentiation.

16493019

http://ansc.umd.edu/faculty/tpresearch.htm

The anterior pituitary is comprised of five major hormone-secreting cell types which differentiate during embryonic development in a temporally distinct manner. Microarrays containing 5,128 unique cDNAs expressed in the neuroendocrine system were produced and used to identify genes with potential involvement in onset of thyroid-stimulating hormone beta-subunit, growth hormone, and prolactin gene transcription during chick embryonic development. We identified 352 cDNAs that were differentially expressed (P < 0.05 and the highest mean at least 1.6-fold greater than the lowest mean) on embryonic day 10, 12, 14, or 17, the period of thyrotroph, somatotroph, and lactotroph differentiation in the chicken. Consistent with cellular ontogeny in the chick anterior pituitary gland, thyroid-stimulating hormone beta-subunit mRNA increased steadily between embryonic day 10 and embryonic day 17, growth hormone mRNA increased between embryonic day 12 and embryonic day 17, and PRL mRNA did not increase until embryonic day 17. Expression of 149 cDNAs increased in a manner similar to thyroid-stimulating hormone beta-subunit mRNA and 67 decreased between embryonic day 10 and embryonic day 17, and some of these are likely associated with thyrotroph differentiation. Similarly, expression of 74 and 66 genes changed in a manner over the 4 ages that is consistent with them having a potential role in induction of growth hormone and prolactin mRNA, respectively. Among these candidate genes are numerous transcription factors and signaling molecules that have not previously been implicated in pituitary development.

Four biological replicates each of chicken pituitary embryonic day 10, embryonic day 12, embryonic day 14, and embryonic day 17 amplified antisense RNA were analyzed using neuroendocrine cDNA microarrays in a reference design. Each experimental sample (embryonic day 10, 12, 14, or 17) was labeled with Cy3 and hybridized with an aliquot of the Cy5 reference pool, which was generated from all sixteen RNA samples.

time course during development

age embryonic day 10

age embryonic day 12

age embryonic day 14

age embryonic day 17