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Sample GSM27917 Query DataSets for GSM27917
Status Public on Aug 13, 2004
Title TAcKLE 200 ng BR (ID378)
Sample type RNA
 
Channel 1
Source name 200 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 200 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 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 0.314787307471764 693 164 114 60 781 224 105 65 0 645 172 128 77 791 248 118 177 0
1627 OL001825 010201 250201 0.584086909891013 9418 2043 119 165 11983 3019 114 116 0 8703 2227 125 860 10478 2720 118 440 0
2479 OL002603 010301 250301 239 162 114 178 262 141 109 119 0 379 125 118 58 441 166 115 71 0
3259 OL003369 010401 250401 0.000309106696387396 3209 684 115 55 4779 844 102 65 0 3097 909 118 54 4766 1016 103 67 0
4111 OL004147 010501 250501 0.126598652339823 4018 641 116 57 4262 1715 111 126 0 3907 341 115 57 4038 426 108 65 0
4891 OL004913 010601 250601 0.133442961287479 274 190 118 54 475 1335 103 87 0 228 125 118 70 419 187 104 70 0
5743 OL005691 010701 250701 210 88 119 64 622 188 110 70 0 229 124 120 154 579 232 109 225 0
6523 OL006457 010801 250801 0.707296853421294 238 113 122 61 648 229 104 71 0 246 143 119 423 597 219 109 166 0
7375 OL007519 010901 250901 462 131 124 56 210 1217 113 67 0 415 109 116 57 228 81 104 65 0
8155 OL008285 011001 251001 124 64 120 92 98 418 109 117 -50 118 51 113 87 75 71 109 140 -50
9007 OL009062 011101 251101 1280 279 113 109 708 239 104 67 0 1221 229 120 104 804 189 116 774 0
9787 OL009826 011201 251201 0.0736077947032472 6925 1298 121 57 2128 462 109 68 0 6540 2052 118 56 2066 644 111 69 0
10639 OL010604 011301 251301 0.104374322470922 8964 1155 124 59 6248 1664 109 68 0 8652 1672 122 56 5866 951 118 216 0
11419 OL011370 011401 251401 15845 3976 134 55 10311 2459 114 84 0 14947 1344 120 201 9732 922 112 126 0
12271 OL012148 011501 251501 154 60 125 56 5259 982 118 68 0 133 73 113 55 4597 974 108 64 0
13051 OL012914 011601 251601 159 639 128 78 142 3769 111 111 -50 127 149 115 56 100 115 110 71 -50
13903 OL013976 011701 251701 -0.319760403142988 126 57 125 64 104 77 106 64 -50 231 104 109 64 199 105 113 69 0
14683 OL014740 011801 251801 136 78 122 57 114 75 114 61 -50 139 73 116 58 108 65 111 65 -50
15535 OL015517 011901 251901 306 146 127 61 807 348 114 64 0 248 109 116 65 730 199 110 70 0
16315 OL016283 012001 252001 -0.13648985627488 8879 1426 125 66 8939 1808 107 62 0 8570 2241 121 68 8611 2447 109 185 0

Total number of rows: 27648

Table truncated, full table size 2821 Kbytes.




Supplementary file Size Download File type/resource
GSM27917-Cy3.tif.gz 58.5 Mb (ftp)(http) TIFF
GSM27917-Cy5.tif.gz 59.0 Mb (ftp)(http) TIFF

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