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Sample GSM230024 Query DataSets for GSM230024
Status Public on Jul 07, 2008
Title KMS12 day6 shIRF4b - repeat 3 - mAdbID:87197
Sample type RNA
 
Channel 1
Source name KMS12 shi_2046 Untreated
Organism Homo sapiens
Characteristics Cell line: KMS12
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 KMS12 shi_2046 day6
Organism Homo sapiens
Characteristics Cell line: KMS12
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: 6 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: 87197
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 0.241 13289 7630 0.00022159737
2 -0.222 3 5 1
3 -0.222 3 5 1
4 -0.222 3 5 1
5 -0.222 3 5 1
6 -0.222 3 5 1
7 -0.222 3 5 1
8 -0.222 3 5 1
9 -0.222 3 5 1
10 -0.301 3 6 0.5367167
11 -0.222 3 5 1
12 -0.124 6068 8078 0.046591893
13 -0.058 7 8 0.83135033
14 -0.168 1789 2633 0.0080533475
15 -0.200 60 95 0.0053890995
16 0.135 19729 14462 0.031316832
17 0.778 138 23 2.3740201e-14
18 0.097 289 231 0.11902796
19 0.059 53630 46788 0.33635467
20 0.000 11 11 0.90156752

Total number of rows: 45015

Table truncated, full table size 1261 Kbytes.




Supplementary file Size Download File type/resource
GSM230024.txt.gz 15.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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