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Sample GSM27926 Query DataSets for GSM27926
Status Public on Aug 13, 2004
Title TAcKLE RT 40 µg RR (ID391)
Sample type RNA
 
Channel 1
Source name 40 µg 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 40 µg universal human reference total RNA, pooled from 10 human cell lines representing distinct tissues (Stratagene #740000)
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Labeling was achieved by reverse transcription with 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 05, 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 -0.090807899120664 530 318 75 88 442 182 133 113 0 477 258 69 90 475 317 137 104 0
1627 OL001825 010201 250201 -0.0249137632800576 4866 1232 74 88 3051 1002 140 109 0 3844 1315 74 90 2566 909 139 100 0
2479 OL002603 010301 250301 -0.0398897804868348 381 149 67 91 363 117 145 111 0 266 88 76 87 260 107 140 115 0
3259 OL003369 010401 250401 -0.148570914945203 2362 958 73 100 1987 772 139 120 0 2176 577 74 71 2058 575 146 102 0
4111 OL004147 010501 250501 -0.198320440730162 556 384 76 90 481 416 144 116 0 685 886 76 84 909 593 148 93 0
4891 OL004913 010601 250601 -0.0510448515519761 1193 1312 73 96 1006 810 148 121 0 308 748 74 101 269 574 145 117 0
5743 OL005691 010701 250701 150 907 76 100 149 620 142 119 -50 195 1188 69 83 216 618 133 109 0
6523 OL006457 010801 250801 0.0608602524789417 200 229 73 85 192 128 148 111 0 246 1089 83 89 360 858 135 110 0
7375 OL007519 010901 250901 -0.0750753876997203 346 218 73 96 277 134 151 132 0 379 953 78 86 379 542 142 107 0
8155 OL008285 011001 251001 -0.182151136339087 229 235 81 94 230 166 148 111 0 357 1083 77 73 589 1200 151 98 0
9007 OL009062 011101 251101 2445 610 81 113 1738 596 155 119 0 2784 2591 79 114 3074 2062 149 105 0
9787 OL009826 011201 251201 0.32561437936375 5336 989 86 110 3745 853 167 129 0 4847 1615 79 89 3664 1417 148 111 0
10639 OL010604 011301 251301 0.168085046235623 3106 2196 87 95 2915 1241 159 136 0 4200 4067 80 90 3986 3015 151 107 0
11419 OL011370 011401 251401 0.0339353578738044 6751 1920 80 86 5323 1683 154 192 0 5678 1709 85 308 5252 1543 164 659 0
12271 OL012148 011501 251501 128 545 83 138 151 335 146 203 -50 113 1147 83 265 159 719 145 560 -50
13051 OL012914 011601 251601 -0.0893475321719484 329 540 81 106 308 298 151 155 0 271 291 76 83 286 204 138 113 0
13903 OL013976 011701 251701 -0.239800357806256 119 104 82 98 143 82 155 138 -50 107 152 85 97 142 127 145 106 -50
14683 OL014740 011801 251801 -0.19355824994625 117 238 81 113 148 152 156 134 -50 123 1668 81 748 204 1274 126 288 0
15535 OL015517 011901 251901 -0.0432400991857653 114 293 87 125 178 213 156 147 -50 176 682 80 135 242 722 139 114 0
16315 OL016283 012001 252001 -0.194444414341233 1168 766 85 128 1202 741 161 153 0 1073 1565 81 65 1259 1592 145 88 0

Total number of rows: 27648

Table truncated, full table size 2879 Kbytes.




Supplementary file Size Download File type/resource
GSM27926-Cy3.tif.gz 58.5 Mb (ftp)(http) TIFF
GSM27926-Cy5.tif.gz 61.3 Mb (ftp)(http) TIFF

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