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Sample GSM1536266 Query DataSets for GSM1536266
Status Public on Nov 04, 2015
Title ILF2 siRNA 1 [exon-level]
Sample type RNA
 
Source name ILF2 siRNA treatment of activated CD4 T cells
Organism Homo sapiens
Characteristics cell type: Primary CD4 T cells
pretreated with: ILF2 siRNA for 24hrs
activated with: anti-CD3/CD26 activator beads for 24 h
passages: 7-8
Treatment protocol Primary CD4 T cells cultured were treated with siRNA 24 hours prior to treatment with anti-CD3/CD26 activator beads (Thermo) for an additional 24 hours.
Growth protocol Primary CD4 T cells cultured for two weeks in RPMI supplemented with 10% FBS, 30U/ml IL2, 100U/ml penicillin and 100mg/ml streptomycin at 37C and 5% CO2
Extracted molecule total RNA
Extraction protocol Cell pellets were resuspended in TRIZOL reagent (Thermo) and the RNA was extracted according to manufacturer's protocol. RNA resuspended in nanopure water was purified over an Rneasy column (QIAGEN) and the polyA RNA was selected using oligo dT beads.
Label biotin
Label protocol Biotinylated cDNA was prepared using the Ambion WT Expression Kit (Ambion) according to the manufacturer's instructions. cDNA was framented and labeled with the GeneChip WT Terminal Labeling Kit (Affymetrix).
 
Hybridization protocol Standard Affymetrix 49 Format Hybridization with 15mg of fragmented cRNA
Scan protocol Affymetrix EukGE-WS2v4 on GCS 3000 7G
Description SAMPLE 16
Data processing Expression intenisties at the probe set (exon) and transcript (gene) level were made with Expression Console (Affymetrix).
Gene level expression intensities were used as input into the R Bioconductor package limma for identification of differentially expressed genes (Ctrl siRNA vs. Specific siRNA)
Exon level expression intensitied were used as input into Alt-Analyze (Emig, et al) to identify differentially spliced exons (Ctrl siRNA vs. Specific siRNA)
The Series supplementary 'TotalRNA_HTA2_all_siRNA_100414.xslx' file has multiple worksheets containing: 1) Differentially expressed genes in ctrl siRNA vs. U2AF1 siRNA; 2)Differntially spliced genes in ctrl siRNA vs. U2AF1 siRNA; 3)Differentially spliced exons in ctrl siRNA vs. U2AF1 siRNA; 4)Differentially expressed genes in ctrl siRNA vs. SRRM2 siRNA; 5)Differntially spliced genes in ctrl siRNA vs. SRRM2 siRNA; 6)Differentially spliced exons in ctrl siRNA vs. SRRM2 siRNA; 7)Differentially expressed genes in ctrl siRNA vs. SYNCRIP siRNA; 8)Differntially spliced genes in ctrl siRNA vs. SYNCRIP siRNA; 9)Differentially spliced exons in ctrl siRNA vs. SYNCRIP siRNA; 10)Differentially expressed genes in ctrl siRNA vs. ILF2 siRNA; 11)Differntially spliced genes in ctrl siRNA vs. ILF2 siRNA; 12)Differentially spliced exons in ctrl siRNA vs. ILF2 siRNA
probe group file: HuEx-1_0-st-v2.r2.pgf
meta-probeset file: HuEx-1_0-st-v2.r2.dt1.hg18.full.mps
 
Submission date Nov 03, 2014
Last update date Nov 04, 2015
Contact name Thomas C Whisenant
E-mail(s) thomas.whisenant@gmail.com
Organization name The Scripps Research Institute
Department Molecular and Experimental Medicine
Lab Salomon
Street address 10550 North Torrey Pines Rd
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL17585
Series (2)
GSE62921 The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells [total RNA-array]
GSE62923 The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells

Data table header descriptions
ID_REF
VALUE Normalized, log-transformed RMA values

Data table
ID_REF VALUE
JUC01000001.hg.1 7.997163
JUC01000002.hg.1 6.610352
JUC01000003.hg.1 9.574502
JUC01000004.hg.1 7.113657
JUC01000005.hg.1 8.814295
JUC01000006.hg.1 8.11439
JUC01000007.hg.1 6.086061
JUC01000008.hg.1 7.056319
JUC01000009.hg.1 4.698166
JUC01000010.hg.1 4.600553
JUC01000011.hg.1 12.63433
JUC01000012.hg.1 9.835154
JUC01000013.hg.1 12.51371
JUC01000014.hg.1 10.34244
JUC01000015.hg.1 6.771631
JUC01000016.hg.1 8.829621
JUC01000017.hg.1 9.038304
JUC01000018.hg.1 8.930075
JUC01000019.hg.1 9.156696
JUC01000020.hg.1 9.156696

Total number of rows: 914585

Table truncated, full table size 23383 Kbytes.




Supplementary file Size Download File type/resource
GSM1536266_051314_TW_7_EPO38_HTA-2_0_.CEL.gz 27.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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