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Sample GSM230025 Query DataSets for GSM230025
Status Public on Jul 07, 2008
Title SKMM1 day2 shIRF4b - mAdbID:87198
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 day2
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: 2 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: 87198
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 0.083 11809 9762 0.18143967
2 -0.301 4 8 0.63950539
3 -0.301 4 8 0.62958658
4 -0.176 4 6 1
5 -0.176 4 6 1
6 -0.176 4 6 1
7 -0.176 4 6 1
8 -0.398 4 10 0.44450465
9 -0.176 4 6 1
10 -0.176 4 6 1
11 -0.176 4 6 1
12 -0.148 2311 3252 0.018410647
13 0.176 9 6 0.65380299
14 -0.092 1828 2261 0.13612583
15 -0.243 24 42 0.038035348
16 -0.006 11706 11879 0.91758615
17 0.141 18 13 0.49773654
18 -0.111 380 491 0.076479785
19 0.102 53357 42166 0.099842034
20 -0.109 14 18 0.62915432

Total number of rows: 45015

Table truncated, full table size 1278 Kbytes.




Supplementary file Size Download File type/resource
GSM230025.txt.gz 15.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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