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Sample GSM1536297 Query DataSets for GSM1536297
Status Public on Nov 04, 2015
Title U2AF2 RIP U2AF1 siRNA 2 [exon-level]
Sample type RNA
 
Source name U2AF2 RIP from U2AF1 siRNA treatment of activated CD4 T cells
Organism Homo sapiens
Characteristics cell type: Primary CD4 T cells
pretreated with: U2AF1 siRNA for 24hrs
activated with: anti-CD3/CD26 activator beads for 24 h
passages: 7-8
rip antibody: U2AF2 antibody
rip antibody vendor: Sigma
rip antibody cat. #: U4758
rip antibody lot #: 034K4841
molecule subtype: U2AF2 RIP RNA
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 5
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 (U2AF2 RIP Ctrl siRNA vs. U2AF2 RIP Specific siRNA)
Exon level expression intensitied were used as input into Alt-Analyze (Emig, et al) to identify differentially spliced exons (U2AFA2 RIP Ctrl siRNA vs. U2AF2 RIP Specific siRNA)
Please note that the 'U2AF2RIP_HTA2_all_siRNA_100414.xlsx' file includes 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. SYNCRIP siRNA; 5)Differntially spliced genes in ctrl siRNA vs. SYNCRIP siRNA; 6)Differentially spliced exons in ctrl siRNA vs. SYNCRIP 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)
GSE62922 The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells [RIP-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 8.310562
JUC01000002.hg.1 7.217036
JUC01000003.hg.1 10.86385
JUC01000004.hg.1 7.82813
JUC01000005.hg.1 9.815745
JUC01000006.hg.1 9.482826
JUC01000007.hg.1 7.500765
JUC01000008.hg.1 7.645339
JUC01000009.hg.1 4.939326
JUC01000010.hg.1 5.278082
JUC01000011.hg.1 13.89835
JUC01000012.hg.1 11.02212
JUC01000013.hg.1 13.89014
JUC01000014.hg.1 12.78708
JUC01000015.hg.1 8.465788
JUC01000016.hg.1 10.62288
JUC01000017.hg.1 11.22802
JUC01000018.hg.1 10.04871
JUC01000019.hg.1 11.04104
JUC01000020.hg.1 11.04104

Total number of rows: 914585

Table truncated, full table size 23383 Kbytes.




Supplementary file Size Download File type/resource
GSM1536297_103113_TW8_7_2_U2AF2_U2AF1_HTA-2_0_.CEL.gz 28.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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