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Sample GSM230026 Query DataSets for GSM230026
Status Public on Jul 07, 2008
Title SKMM1 day4 shIRF4b - mAdbID:87199
Sample type RNA
 
Channel 1
Source name SKMM1 shi_2046 Untreated
Organism Homo sapiens
Characteristics Cell line: SKMM1
Cell type: myeloma
Disease state: myeloma
genotype/variation: shirf4_2046 (shIRFb)
Extracted molecule total RNA
Extraction protocol Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
Label cy3
Label protocol Agilent Labeling-Cy3
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
Channel 2
Source name SKMM1 shi_2046 day4
Organism Homo sapiens
Characteristics Cell line: SKMM1
Cell type: myeloma
Disease state: myeloma
genotype/variation: shirf4_2046 (shIRFb)
Treatment protocol Treatment type: compound
Agent: doxycycline
Treatment dose: 20 ng/ml
Treatment time: 4 days
Treatment temperature: 37c
Extracted molecule total RNA
Extraction protocol Trizol Total RNA
Extraction method: Trizol
Other: Total RNA was extracted using Trizol according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
Label cy5
Label protocol Agilent Labeling-Cy5
Other: Total RNA was reverse transcribed to cDNA using T7 Promoter Primer and MMLV-RT. Then the cDNA was converted to aRNA polymerase, which simultaneously amplifies target material and incorporates cyanine 3- or cyanine 5-labeled CTP (Two-Color Microarray-Based Gene Expression Analysis Protocol, Agilent).
 
 
Hybridization protocol Agilent Hybridization
Other: According to the manufacture's recommended protocol (Two-Color Microarray-Based Gene Expression Analysis, Agilent).
Scan protocol Agilent Scanning Protocol
Other: Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2505B, Agilent) using the default settings for 4x44k format two-color arrays.
Description mAdb experiment ID: 87199
Data processing Agilent Data Processing Protocol
Calculation Method: Images were auto gridded, analyzed and data extracted using Agilent Feature Extraction Software (Version 9.1.3.1). Spot values were normalized using the default linear-lowess normalization.
 
Submission date Sep 17, 2007
Last update date Aug 14, 2011
Contact name Louis M. Staudt
E-mail(s) lstaudt@mail.nih.gov
Phone 301-402-1892
Organization name National Cancer Institute
Department Lymphoid Malignancies Branch
Lab Louis M Staudt
Street address 9000 Rockville Pike, Bldg 10, Rm 4N114
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
 
Platform ID GPL4133
Series (1)
GSE9067 Myeloma IRF4 target genes - Agilent

Data table header descriptions
ID_REF Agilent ID
VALUE linear-lowess normalized log10 ratio (Cy5/Cy3)
rDyeNormSignal Red Channel Signal (linear-lowess normalized)
gDyeNormSignal Green Channel Signal (linear-lowess normalized)
PValueLogRatio significance level of the log ratio

Data table
ID_REF VALUE rDyeNormSignal gDyeNormSignal PValueLogRatio
1 0.041 7903 7196 0.5081436
2 -0.368 3 7 1
3 -0.368 3 7 1
4 -0.368 3 7 1
5 -0.368 3 7 1
6 -0.544 2 7 1
7 -0.544 2 7 1
8 -0.544 2 7 1
9 -0.602 2 8 0.43630645
10 -0.699 2 10 0.28088546
11 -0.544 2 7 0.47380236
12 -0.353 1056 2378 3.7482565e-07
13 -0.497 7 22 0.051793911
14 0.079 1531 1277 0.20158249
15 0.023 19 18 0.92473543
16 0.059 10702 9333 0.33500192
17 -0.125 15 20 0.52126199
18 -0.035 325 352 0.57412189
19 0.276 41103 21756 3.1831132e-05
20 -0.333 13 28 0.04531699

Total number of rows: 45015

Table truncated, full table size 1265 Kbytes.




Supplementary file Size Download File type/resource
GSM230026.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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