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Sample GSM27818 Query DataSets for GSM27818
Status Public on Aug 13, 2004
Title TAcKLE 20 ng RR (ID370)
Sample type RNA
 
Channel 1
Source name 20 ng universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000)
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name 20 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) [email protected]
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 -0.102923003842014 557 176 96 60 471 191 85 68 0 1052 502 97 124 943 454 96 194 0
1627 OL001825 010201 250201 0.177301931265313 12782 4505 102 67 13839 4395 85 55 0 12495 4692 93 144 13889 4366 96 185 0
2479 OL002603 010301 250301 0.189143672131289 121 102 95 63 83 62 85 55 -50 101 138 97 52 87 57 92 54 -50
3259 OL003369 010401 250401 0.145488746020503 1030 252 90 65 1063 269 87 55 0 840 273 97 54 829 252 91 54 0
4111 OL004147 010501 250501 0.155524320560307 2328 485 89 48 2184 338 73 47 0 3055 1471 94 56 3022 1317 93 57 0
4891 OL004913 010601 250601 -0.107194629866155 270 171 77 44 194 112 71 49 0 114 87 93 56 89 57 94 59 -50
5743 OL005691 010701 250701 245 237 85 57 133 135 79 50 0 199 195 88 46 124 239 92 53 0
6523 OL006457 010801 250801 -0.0891879944458616 92 56 90 63 84 47 87 51 -50 205 154 96 51 218 211 90 53 0
7375 OL007519 010901 250901 0.0859328368036474 431 139 92 57 395 135 90 57 0 524 594 97 98 454 733 95 59 0
8155 OL008285 011001 251001 -0.0661254372239033 204 291 97 60 152 178 88 53 0 117 63 97 57 85 56 94 57 -50
9007 OL009062 011101 251101 555 252 92 53 633 222 91 55 0 434 152 94 123 468 177 94 172 0
9787 OL009826 011201 251201 -0.175425560609981 7748 2641 98 50 8131 2203 92 52 0 6641 1820 95 121 6749 1438 93 171 0
10639 OL010604 011301 251301 -0.00235199688292731 7074 1477 95 53 6623 865 87 55 0 6772 1583 94 47 5736 1417 92 53 0
11419 OL011370 011401 251401 -0.137373540777562 7093 1604 98 955 6595 1403 88 54 0 6281 1309 97 55 6474 1117 92 53 0
12271 OL012148 011501 251501 102 49 94 750 76 46 89 58 -50 89 55 97 50 74 54 97 55 -50
13051 OL012914 011601 251601 115 63 95 53 82 48 88 52 -50 102 60 95 51 85 53 96 95 -50
13903 OL013976 011701 251701 0.0381313301419404 109 63 95 64 96 57 88 53 -50 247 97 95 50 232 100 89 81 0
14683 OL014740 011801 251801 -0.21936661841688 174 79 92 48 167 90 82 50 0 105 61 99 176 108 80 94 106 -50
15535 OL015517 011901 251901 -0.0889963521231891 231 73 98 53 134 69 85 50 0 142 95 95 77 94 70 94 58 -50
16315 OL016283 012001 252001 0.0650145301877747 6394 2002 99 59 6839 1922 87 54 0 5400 1927 95 77 4907 1664 93 52 0

Total number of rows: 27648

Table truncated, full table size 2770 Kbytes.




Supplementary file Size Download File type/resource
GSM27818-Cy3.tif.gz 58.8 Mb (ftp)(http) TIFF
GSM27818-Cy5.tif.gz 58.2 Mb (ftp)(http) TIFF

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