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Sample GSM27835 Query DataSets for GSM27835
Status Public on Aug 13, 2004
Title TAcKLE 2 ng BR (ID372)
Sample type RNA
 
Channel 1
Source name 2 ng total RNA extracted from normal breast tissue of a 56 year old female body (Stratagene #735044)
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name 2 ng universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000)
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description aRNA produced by T7 amplification was reversely transcribed and subsequently labeled using Klenow fragment and Cy-dUTPs. Hybridization was carried out at 37 °C in UltraHyb buffer (Ambion) on a GeneTAC hybridization station (Genomic Solutions).
Keywords = amplification
Keywords = labeling
Keywords = protocol
Keywords = spotted
Keywords = human
Keywords = long oligonucleotide
Keywords = oligo
Keywords = 70mer
Keywords = Operon
Lot batch =
 
Submission date Aug 04, 2004
Last update date Oct 28, 2005
Contact name Joerg Schlingemann
E-mail(s) j.schlingemann@dkfz.de
Phone +49 6221 424672
Fax +49 6221 424639
URL http://www.dkfz-heidelberg.de/kompl_genome/index.html
Organization name German Cancer Research Center (DKFZ)
Department Molecular Biology (B060)
Lab Expression Profiling Facility
Street address Technologiepark III, Im Neuenheimer Feld 280
City Heidelberg
ZIP/Postal code 69120
Country Germany
 
Platform ID GPL1384
Series (1)
GSE1645 TAcKLE - Transcriptome Amplification and cDNA Labeling for Expression analysis

Data table header descriptions
ID_REF
CLONE_Y_ID DKFZ database ID (CloneY)
CHIPYARD_ID_1 DKFZ database ID (ChipYard) and position of spot replicate 1: block, column, row
CHIPYARD_ID_2 DKFZ database ID (ChipYard) and position of spot replicate 2: block, column, row
VALUE log2-transformed normalized expression ratio (Cy5/Cy3); spot replicates were averaged. Spots not recognized by the image analysis software "GenePix Pro 5.0" (Axon Instruments) were excluded from the calculations. Raw fluorescence intensities were normalized applying the variance stabilization method (W. Huber et al., Bioinformatics 18 Suppl. 1, 2002). To eliminate low quality data, the data points were ranked according to spot homogeneity, as assayed by the ratio of median to mean fluorescence intensity, the ratio of spot to local background intensity and the standard deviation of the log2 ratios between spot replicates. Those data points ranked among the lower 20% were removed from the data set. Genes that could not be quantified in more than 33% of all experiments of the experimental series after filtering were excluded as well.
CH1_RAW_SPOT1 Cy3 raw fluorescence intensity for spot replicate 1
CH1_SD_SPOT1 standard deviation of Cy3 raw fluorescence intensity for spot replicate 1
CH1_BKD_RAW_SPOT1 Cy3 raw fluorescence intensity for local background of spot replicate 1
CH1_BKD_SD_SPOT1 standard deviation of Cy3 raw fluorescence intensity for local background of spot replicate 1
CH2_RAW_SPOT1 Cy5 raw fluorescence intensity for spot replicate 1
CH2_SD_SPOT1 standard deviation of Cy5 raw fluorescence intensity for spot replicate 1
CH2_BKD_RAW_SPOT1 Cy5 raw fluorescence intensity for local background of spot replicate 1
CH2_BKD_SD_SPOT1 standard deviation of Cy5 raw fluorescence intensity for local background of spot replicate 1
FLAGS_SPOT1 GenePix flag for spot replicate 1
CH1_RAW_SPOT2 Cy3 raw fluorescence intensity for spot replicate 2
CH1_SD_SPOT2 standard deviation of Cy3 raw fluorescence intensity for spot replicate 2
CH1_BKD_RAW_SPOT2 Cy3 raw fluorescence intensity for local background of spot replicate 2
CH1_BKD_SD_SPOT2 standard deviation of Cy3 raw fluorescence intensity for local background of spot replicate 2
CH2_RAW_SPOT2 Cy5 raw fluorescence intensity for spot replicate 2
CH2_SD_SPOT2 standard deviation of Cy5 raw fluorescence intensity for spot replicate 2
CH2_BKD_RAW_SPOT2 Cy5 raw fluorescence intensity for local background of spot replicate 2
CH2_BKD_SD_SPOT2 standard deviation of Cy5 raw fluorescence intensity for local background of spot replicate 2
FLAGS_SPOT2 GenePix flag for spot replicate 2

Data table
ID_REF CLONE_Y_ID CHIPYARD_ID_1 CHIPYARD_ID_2 VALUE CH1_RAW_SPOT1 CH1_SD_SPOT1 CH1_BKD_RAW_SPOT1 CH1_BKD_SD_SPOT1 CH2_RAW_SPOT1 CH2_SD_SPOT1 CH2_BKD_RAW_SPOT1 CH2_BKD_SD_SPOT1 FLAGS_SPOT1 CH1_RAW_SPOT2 CH1_SD_SPOT2 CH1_BKD_RAW_SPOT2 CH1_BKD_SD_SPOT2 CH2_RAW_SPOT2 CH2_SD_SPOT2 CH2_BKD_RAW_SPOT2 CH2_BKD_SD_SPOT2 FLAGS_SPOT2
847 OL001060 010101 250101 0.82176693809778 290 97 88 37 606 179 79 53 0 240 72 84 36 450 163 89 52 0
1627 OL001825 010201 250201 -0.41022884307592 8347 994 88 39 9367 1766 90 101 0 6684 1091 91 40 7613 1716 91 57 0
2479 OL002603 010301 250301 287 105 87 39 314 135 83 52 0 246 93 91 50 272 105 87 55 0
3259 OL003369 010401 250401 -0.0345678347431031 1013 246 82 80 1229 305 83 59 0 812 315 91 38 1124 432 90 51 0
4111 OL004147 010501 250501 -0.905494120160115 1543 278 83 36 1388 351 94 54 0 1355 432 90 38 1388 609 89 52 0
4891 OL004913 010601 250601 -0.0180203202187146 78 47 88 49 133 86 86 54 -50 72 34 89 40 152 84 90 53 -50
5743 OL005691 010701 250701 70 30 84 37 281 119 86 50 0 67 29 90 42 287 102 86 52 0
6523 OL006457 010801 250801 0.255352409863900 96 54 81 38 598 179 88 53 0 99 106 94 40 508 231 92 52 0
7375 OL007519 010901 250901 2.30754985438246 252 545 82 37 200 162 82 52 0 228 76 90 38 190 83 92 55 0
8155 OL008285 011001 251001 88 77 85 501 71 51 89 61 -50 92 51 90 36 73 47 93 58 -50
9007 OL009062 011101 251101 380 119 84 37 174 94 90 48 0 328 97 91 37 209 91 91 56 0
9787 OL009826 011201 251201 5536 1119 89 39 2302 649 87 52 0 5096 956 93 40 2030 506 93 58 0
10639 OL010604 011301 251301 0.0216349411350745 5165 910 91 40 2931 784 89 51 0 5612 615 91 825 3753 847 94 193 0
11419 OL011370 011401 251401 1.51416283225481 11343 2564 89 45 5860 1269 87 54 0 10707 1348 93 41 5791 1239 91 65 0
12271 OL012148 011501 251501 76 34 88 35 1627 334 89 52 0 81 43 93 43 1686 360 88 53 0
13051 OL012914 011601 251601 0.34735268959633 79 36 89 36 76 54 85 53 -50 83 43 95 49 74 42 90 57 -50
13903 OL013976 011701 251701 -0.971149753262312 221 77 83 45 162 65 80 51 0 197 105 92 71 147 95 93 198 0
14683 OL014740 011801 251801 -1.77362070020997 87 40 88 41 60 49 86 53 -50 83 40 93 62 61 44 94 160 -50
15535 OL015517 011901 251901 210 108 88 97 341 120 86 58 0 185 66 92 120 335 112 97 130 0
16315 OL016283 012001 252001 0.210618119100085 6166 887 92 38 3326 764 89 52 0 5350 1554 93 141 3260 719 101 163 0

Total number of rows: 27648

Table truncated, full table size 2703 Kbytes.




Supplementary file Size Download File type/resource
GSM27835-Cy3.tif.gz 57.0 Mb (ftp)(http) TIFF
GSM27835-Cy5.tif.gz 58.2 Mb (ftp)(http) TIFF

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