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Sample GSM517058 Query DataSets for GSM517058
Status Public on May 27, 2010
Title HF-23897-(1), Affymetrix HG-U133 plus 2.0 array
Sample type RNA
Source name HF-23897-(1)
Organism Homo sapiens
Characteristics organ: Adjacent Normal
Extracted molecule total RNA
Extraction protocol Qiagen AllPrep extraction kit was used according to the manufacturer's instructions
Label biotin
Label protocol 3 ug of total RNA was converted to double-stranded cDNA using Invitrogen's SuperScript Choice kit. cDNA was purified using Affymterix Sample Cleanup Module kit and used to generate biotin labeled cRNA with Enzo in vitro transcription kit. The labeled cRNA was purified using Affymetrix Sample Cleanup Module kit.
Hybridization protocol 10 ug of labeled cRNA was fragmented and hybridized to the arrays following manufacturer's protocol (Affymterix).
Scan protocol Affymetrix user manual (GeneChip scanner 3000)
Description none
Data processing Raw data were processed with the MAS5.0 method to obtain normalized probe set summaries. Values for each sample were scaled to mean, trimmed 2%, of 500.
Submission date Mar 01, 2010
Last update date Jul 11, 2012
Contact name Peter Haverty
Organization name Genentech, Inc.
Department Bioinformatics
Street address 1 DNA Way
City South San Francisco
State/province CA
ZIP/Postal code 94080
Country USA
Platform ID GPL570
Series (2)
GSE20578 Assessment of mutation on expression levels
GSE20585 The mutation spectrum revealed by paired genome sequences from a lung cancer patient

Data table header descriptions
VALUE MAS5.0 signal
p-value Affymetrix "sig_p" p-values, p-value expression is above background

Data table
ID_REF VALUE p-value
AFFX-BioB-5_at 797.2290649 0.0011
AFFX-BioB-M_at 1019.774292 0.00075
AFFX-BioB-3_at 358.4300537 0.00321
AFFX-BioC-5_at 1712.900879 9.00E-05
AFFX-BioC-3_at 1882.600098 4.00E-05
AFFX-BioDn-5_at 2469.93335 6.00E-05
AFFX-BioDn-3_at 7421.208984 0.00013
AFFX-CreX-5_at 25744.2168 5.00E-05
AFFX-CreX-3_at 23517.55469 4.00E-05
AFFX-DapX-5_at 2722.912354 5.00E-05
AFFX-DapX-M_at 3682.420898 0.00034
AFFX-DapX-3_at 7066.727051 7.00E-05
AFFX-LysX-5_at 348.2886963 0.00017
AFFX-LysX-M_at 581.0053711 0.01255
AFFX-LysX-3_at 1160.140381 4.00E-05
AFFX-PheX-5_at 276.6276245 0.00045
AFFX-PheX-M_at 660.9276123 0.00086
AFFX-PheX-3_at 570.0010376 0.00039
AFFX-ThrX-5_at 335.7828979 0.00556
AFFX-ThrX-M_at 588.1029053 0.00017

Total number of rows: 54675

Table truncated, full table size 1765 Kbytes.

Supplementary file Size Download File type/resource
GSM517058.CEL.gz 9.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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