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Sample GSM1536239 Query DataSets for GSM1536239
Status Public on Nov 04, 2015
Title U2AF2 RIP-Seq R91 R 1
Sample type SRA
 
Source name primary CD4 T cell culture
Organism Homo sapiens
Characteristics cell type: primary CD4 T cell culture
activation: none
passages: 7-8
rip antibody: U2AF2 antibody
rip antibody vendor: Sigma
rip antibody cat. #: U4758
rip antibody lot #: 034K4841
molecule subtype: U2AF2 RIP RNA
barcode: TTCAGC
run: 91
Treatment protocol Primary CD4 T cells cultured were treated with anti-CD3/CD26 activator beads (Thermo) for 0 or 48 hours. Lysates from the cell pellets for both conditions were used as input into U2AF2 RIP.
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 Eluate from U2AF2 RIP was combined with 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).
Script- Seq v2 (Epicentre) with an input of 50ng U2AF2 RIP RNA
 
Library strategy RIP-Seq
Library source transcriptomic
Library selection other
Instrument model Illumina HiSeq 2000
 
Description U2AF2 RIP from resting CD4 T cells
Data processing Basecalls performed using CASAVA version 1.7-1.8.1
Raw reads were quality filtered (q > 25) and 3' adapters were removed using trimgalore version 0.2.7 - trim_galore -q 25 --phred33 --paired --trim1 -a GATCGGAAGAGCACACGTCTGAACTCCAGTC --retain_unpaired forward.fastq reverse.fastq
Reads were aligned to hg19 using Tophat version 2.0.9 - tophat --b2-very-sensitive --prefilter-multihits -G genes.gtf --coverage-search
Aligned reads were quality filtered using picard (markDuplicates) version 1.9
Aligned reads were filtered for quality (q < 20) using samtools
Filtered aligned reads were assigned to genes and analyzed for differential expresson/binding (Resting vs. Activated) according to the vignette for the R Bioconductor package edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet with 3 worksheets: 1) All U2AF2 bound genes; 2) Differentially expressed "bound" genes with adjusted p-value < 0.05 (edgeR)
 
Submission date Nov 03, 2014
Last update date May 15, 2019
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 GPL11154
Series (2)
GSE62919 The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells [RIP-Seq]
GSE62923 The Activation-Induced Assembly of an RNA/Protein Interactome Centered on the Splicing Factor U2AF2 Regulates Gene Expression in Human CD4 T Cells
Relations
BioSample SAMN03159528
SRA SRX749864

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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