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Sample GSM1536293 Query DataSets for GSM1536293
Status Public on Nov 04, 2015
Title U2AF2 RIP Control siRNA 1 [exon-level]
Sample type RNA
 
Source name U2AF2 RIP from Control siRNA treatment of activated CD4 T cells
Organism Homo sapiens
Characteristics cell type: Primary CD4 T cells
pretreated with: Control 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 1
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 8.656321
JUC01000002.hg.1 6.935225
JUC01000003.hg.1 11.13843
JUC01000004.hg.1 6.894884
JUC01000005.hg.1 9.512756
JUC01000006.hg.1 9.382936
JUC01000007.hg.1 7.218285
JUC01000008.hg.1 6.906422
JUC01000009.hg.1 4.991936
JUC01000010.hg.1 5.857337
JUC01000011.hg.1 13.79267
JUC01000012.hg.1 10.80184
JUC01000013.hg.1 13.84318
JUC01000014.hg.1 12.59502
JUC01000015.hg.1 8.697025
JUC01000016.hg.1 10.88124
JUC01000017.hg.1 10.19833
JUC01000018.hg.1 9.861104
JUC01000019.hg.1 10.93504
JUC01000020.hg.1 10.93504

Total number of rows: 914585

Table truncated, full table size 23383 Kbytes.




Supplementary file Size Download File type/resource
GSM1536293_103113_TW4_7_1_U2AF2_NEG_HTA-2_0_.CEL.gz 28.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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