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Sample GSM88376 Query DataSets for GSM88376
Status Public on May 01, 2006
Title Livers from fat line chickens, pool 6, replicate 2
Sample type RNA
 
Channel 1
Source name Livers from fat line chickens
Organism Gallus gallus
Characteristics Livers from four fat line chickens with 2.3 % (mean) of adipose tissue content per live body weight
Extracted molecule polyA RNA
Extraction protocol Total RNA were extracted with TRIzol Reagent (Invitrogen) from 4 chickens. Poly(A)+ RNA was extracted from a pool of the 4 total RNA preparations with PolyATtract® mRNA isolation system III (Promega)
Label Cy5
Label protocol Poly(A)+ RNA (500 ng) were reverse-transcribed with amino-allyl-dUTPs (CyScribe Post-Labeling Kit, Amersham Biosciences). The amino-allyl modified cDNAs were purified on GFX columns (GFX Purification Kit, Amersham Biosciences) and further labelled by incubation with cyanine dyes (Cy3 or Cy5). Labeled cDNAs were also purified on GFX columns and mixed with hybridization buffer (5X Denhardt’s, 3.5X SSC, 0.3 % SDS, 0.5 µg/µl yeast RNA, 0.5 µg/µl poly(A) RNA and 50 % formamide)
 
Channel 2
Source name Livers from all lean and fat line chickens
Organism Gallus gallus
Characteristics As a reference sample, poly(A)+ RNA preparations from all lean and fat line chickens (10) were mixed in a superpool.
Extracted molecule polyA RNA
Extraction protocol pooling of poly(A)+ RNA prepared from ten lean and fat line chicken liver total RNA pools
Label Cy3
Label protocol Poly(A)+ RNA (500 ng) were reverse-transcribed with amino-allyl-dUTPs (CyScribe Post-Labeling Kit, Amersham Biosciences). The amino-allyl modified cDNAs were purified on GFX columns (GFX Purification Kit, Amersham Biosciences) and further labelled by incubation with cyanine dyes (Cy3 or Cy5). Labeled cDNAs were also purified on GFX columns and mixed with hybridization buffer (5X Denhardt’s, 3.5X SSC, 0.3 % SDS, 0.5 µg/µl yeast RNA, 0.5 µg/µl poly(A) RNA and 50 % formamide)
 
 
Hybridization protocol Test sample labelled with Cy5 and reference sample labelled with Cy3 solutions (10 µl) were mixed and incubated 2 min at 100°C, and 30 min at 37°C before hybridization. Hybridizations were performed in hybridization chambers (Corning Life Sciences) overnight at 42°C and slides were washed in 2X SSC, 0.1 % SDS, then in 1X SSC and finally twice in 0.2X SSC.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with ScanArray 4000 XL (Packard Biochip Technologies) fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0.1.17 analysis software.
Description Livers from fat line chickens, pool 6, replicate 2
Data processing After background correction and removal of flagged values, log base 2 expression ratios were normalized by lowess fitness using Madtools.
 
Submission date Dec 19, 2005
Last update date Dec 19, 2005
Contact name Christian Diot
E-mail(s) Christian.Diot@rennes.inra.fr
Organization name INRA
Department Animal Genetics
Lab UMR Génétique Animale
Street address 65, rue de saint-Brieuc, CS 84215
City Rennes cedex
ZIP/Postal code 35042
Country France
 
Platform ID GPL3265
Series (1)
GSE3867 Gene expression in chicken livers from lean and fat lines

Data table header descriptions
ID_REF
VALUE Normalized log2 ratio of median defined by CH1/CH2
CH1_median CH1 (F635) median fluorescence intensity
CH1_MEAN CH1 (F635) mean fluorescence intensity
CH1_SD CH1 (F635) fluorescence intensity standard deviation
CH1_BKD_Median CH1 (F635) background median fluorescence intensity
CH1_BKD_MEAN CH1 (F635) background mean fluorescence intensity
CH1_BKD_SD CH1 (F635) background fluorescence intensity standard deviation
% > CH1_BKD_+2SD % of feature pixels greater than two standard deviations over the background
CH2_median CH2 (F532) median fluorescence intensity
CH2_MEAN CH2 (F532) mean fluorescence intensity
CH2_SD CH2 (F532) fluorescence intensity standard deviation
CH2_BKD_Median CH2 (F532) background median fluorescence intensity
CH2_BKD_MEAN CH2 (F532) background mean fluorescence intensity
CH2_BKD_SD CH2 (F532) background fluorescence intensity standard deviation
% > CH2_BKD_+2SD % of feature pixels greater than two standard deviations over the background
Ratio of Medians (635/532) Unnormalized ratio of medians defined by CH1/CH2
Ratio of Means (635/532) Unnormalized ratio of means defined by CH1/CH2
AREA Number of feature pixels
BKD_AREA Number of feature background pixels
CH1_Median - CH1_BKD Channel 1 median signal
CH2_Median - CH2_BKD Channel 2 median signal
CH1_Mean - CH1_BKD Channel 1 mean signal
CH2_Mean - CH2_BKD Channel 2 mean signal

Data table
ID_REF VALUE CH1_median CH1_MEAN CH1_SD CH1_BKD_Median CH1_BKD_MEAN CH1_BKD_SD % > CH1_BKD_+2SD CH2_median CH2_MEAN CH2_SD CH2_BKD_Median CH2_BKD_MEAN CH2_BKD_SD % > CH2_BKD_+2SD Ratio of Medians (635/532) Ratio of Means (635/532) AREA BKD_AREA CH1_Median - CH1_BKD CH2_Median - CH2_BKD CH1_Mean - CH1_BKD CH2_Mean - CH2_BKD
1.1.1 null 0 200 359 0 178 416 7 14181 16879 12599 124 529 824 97 0.000 0.012 80 464 0 14057 200 16755
1.2.1 null 48 356 543 0 239 437 15 385 739 835 25 421 678 23 0.133 0.499 52 400 48 360 356 714
1.3.1 0.06 21735 20945 9636 773 1117 1202 100 17191 16192 7346 1255 1681 1604 96 1.315 1.350 80 550 20962 15936 20172 14937
1.4.1 -0.16 14583 14212 7837 0 354 598 98 10083 11105 6902 79 526 873 96 1.458 1.289 80 514 14583 10004 14212 11026
1.5.1 -0.07 7487 7948 6391 0 237 448 88 6065 6530 5186 964 1324 1343 60 1.468 1.428 80 480 7487 5101 7948 5566
1.6.1 0.33 21447 21541 7386 0 888 2311 100 19692 19733 7245 0 629 1527 100 1.089 1.092 52 366 21447 19692 21541 19733
1.7.1 0.03 13729 14104 6451 0 179 397 100 10485 10821 5721 0 226 490 99 1.309 1.303 120 675 13729 10485 14104 10821
1.8.1 -0.03 7269 7125 3972 0 166 363 97 5060 5227 3442 0 220 503 86 1.437 1.363 80 502 7269 5060 7125 5227
1.9.1 -0.05 31665 31240 12589 0 401 891 100 23808 23485 10234 0 373 693 100 1.330 1.330 80 512 31665 23808 31240 23485
1.10.1 -0.15 26834 25070 10662 0 328 635 100 18740 18408 10406 0 362 754 98 1.432 1.362 52 384 26834 18740 25070 18408
1.11.1 -0.12 3632 4354 3539 0 210 455 80 2564 3318 2728 0 252 608 78 1.417 1.312 80 480 3632 2564 4354 3318
1.12.1 null 0 172 368 0 105 326 11 0 252 588 0 230 511 7 0.000 0.683 52 392 0 0 172 252
1.1.2 null 65535 60255 11916 222 678 1555 100 65535 53586 17552 352 821 1312 100 1.002 1.128 80 558 65313 65183 60033 53234
1.2.2 -0.02 9450 9302 4466 0 227 442 96 7317 7710 3731 243 633 889 92 1.336 1.246 52 340 9450 7074 9302 7467
1.3.2 null 835 1032 883 651 1567 5882 0 1410 1773 1437 791 1598 3843 0 0.297 0.388 52 420 184 619 381 982
1.4.2 null 65535 56964 14708 741 1485 3210 100 65535 50750 20305 899 1502 2267 100 1.002 1.128 52 420 64794 64636 56223 49851
1.5.2 null 2133 2830 2981 0 221 496 88 1443 2185 3267 211 707 1078 30 1.731 1.434 80 560 2133 1232 2830 1974
1.6.2 null 1073 1443 1539 0 186 396 56 1644 2059 1856 363 796 1089 30 0.838 0.851 120 820 1073 1281 1443 1696
1.7.2 0.40 9265 9525 4948 0 163 383 100 8768 8935 4647 0 242 531 97 1.057 1.066 80 560 9265 8768 9525 8935
1.8.2 null 721 1027 832 0 187 421 48 794 1200 1230 0 287 582 36 0.908 0.856 52 340 721 794 1027 1200

Total number of rows: 1728

Table truncated, full table size 175 Kbytes.




Supplementary data files not provided

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