|
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
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Library strategy |
RIP-Seq |
Library source |
transcriptomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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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)
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|
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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 |