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Series GSE52834 Query DataSets for GSE52834
Status Public on Dec 01, 2014
Title Analysis of pre-mRNA splicing trans-regulation in human lymphoblastoid cell lines
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary To understand the role of trans factors in the regulation of splicing and alternative splicing, we knocked-down 22 RNA-binding proteins previously shown or suspected to be involved in the regulation of splicing (“splicing factors”). We performed knockdown experiments in triplicate in the Hapmap lymphoblastoid cell line GM19238 using small interfering RNAs (siRNAs). RNA was extracted 72 hours after knockdown for RNA-seq library preparation. The following splicing factors were analyzed: ACIN1, ADAR, HNRPA2B1, HNRPF, HNRPH1, HNRPH2, HNRPK, HNRPL, HNRPR, PCBP2, PTBP1, RBM23, RBM39, RBMX, RNPS1, SRSF1, SRSF3, SRSF4, SRSF8, SRSF9, SRSF10 and SYNCRIP. Seven controls were generated with non-specific siRNA probes transfection. RNA-seq libraries were multiplexed and sequenced on 3 different flow-cells on an Illumina HiSeq 2000 sequencer (single-end 107 bp long reads).
 
Overall design 73 samples, including 3 replicates for each of the 22 knockdowns and 7 controls
 
Contributor(s) Roux J, Pavlovic B, Pritchard JK, Gilad Y
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Submission date Nov 29, 2013
Last update date May 15, 2019
Contact name Julien Roux
E-mail(s) julien.roux@unibas.ch
Organization name University of Basel
Department Department of Biomedicine
Street address Hebelstrasse 20
City Basel
ZIP/Postal code 4031
Country Switzerland
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (73)
GSM1276840 2_A
GSM1276841 2_G
GSM1276842 2_PTBP1_D
Relations
BioProject PRJNA230267
SRA SRP033393

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE52834_RPKM.txt.gz 13.9 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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