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Sample GSM841734 Query DataSets for GSM841734
Status Public on May 02, 2012
Title AFF4 shRNA rep 1 RNA-seq
Sample type SRA
 
Source name AFF4 shRNA RNA-seq
Organism Homo sapiens
Characteristics cell line: HEK293T
cell type: human embryonic kidney cells
transfected with: AFF4 SMARTpool siRNA duplex
Treatment protocol HEK293T cells were transfected with AFF2, AFF3, or AFF4 SMARTpool siRNA duplex (Dharmacon) using Lipofectamine (Invitrogen). AFF2 shRNA (V2THS_113929), AFF3 shRNA (V2THS_133851), and AFF4 shRNA (V2THS_197522) and constructs were purchased from Open Biosystems. Lentiviral particle preparation and infection were performed as previously described (Lin et al. 2010). Total RNA was extracted with the RNeasy kit from Qiagen and residual DNA was digested with RNase-free DNase I (Sigma) before re-purification by the RNeasy kit.
Growth protocol HEK293T cells were cultured in DMEM supplemented with 10% FBS. Cells were maintained at 37 °C under 5% CO2
Extracted molecule polyA RNA
Extraction protocol Total RNA was prepared from the shRNA stable cell lines, and biological duplicate experiments were performed. Polyadenylated RNA was purified from total RNA and fragmented. Double-stranded cDNA from the RNA fragments were ligated to adapters and subjected to deep sequencing (Illumina GA IIx).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
 
Description AFF4_shRNA_1
Data processing H4-1.bam; genome build: hg19
RNA-seq analysis was done using TopHat v1.3.2 (Trapnell et al. 2009) and Bowtie v0.12.7. Human transcript annotations were from RefSeq (downloaded from UCSC on Jan 21, 2011). Differentially expressed genes after RNAi were called with a FDRadjusted p-value < 0.05 and MA plots were determined by Cufflinks v1.1.0 (Trapnell et al. 2010). Paired-end read fragment insert lengths were estimated at a mean of 205 with a standard deviation of 145. Four non-targeting RNAi samples were used as the control samples. Each RNAi sample was done with two replicates.
 
Submission date Dec 02, 2011
Last update date May 15, 2019
Contact name Alexander (Garrett) Garruss
E-mail(s) asg@stowers.org
Organization name Stowers Institute for Medical Research
Lab Shilatifard
Street address 1000 East 50th Street
City Kansas CIty
State/province Missouri
ZIP/Postal code 64110
Country USA
 
Platform ID GPL10999
Series (1)
GSE34097 The SEC family of RNA Polymerase II elongation factors: gene target specificity and transcriptional output
Relations
SRA SRX110228
BioSample SAMN00761671

Supplementary file Size Download File type/resource
GSM841734_H4-1.bam 1.6 Gb (ftp)(http) BAM
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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