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Series GSE59335 Query DataSets for GSE59335
Status Public on Jul 12, 2014
Title Investigation into human Tra2 protein-dependent splicing in MDA-MB-231 cells using iCLIP and RNA-seq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Alternative splicing—the production of multiple mRNA isoforms from a single gene—is regulated in part by RNA-binding proteins (RBPs). While the RBPs Tra2α and Tra2β have both been implicated in the regulation of alternative splicing, their relative contribution to this process are not well understood. Here we use iCLIP to identify Tra2β target exons in MDA-MB-231 cells. We find that simultaneous—but not individual—depletion of Tra2α and Tra2β induces substantial shifts in the splicing pattern of endogenous Tra2β target exons identified by iCLIP. We next use RNA-seq following joint Tra2 protein depletion to comprehensively identify Tra2 protein-dependent exons in MDA-MB-231 cells.
Overall design Endogenous Tra2β binding sites were mapped across the MDA-MB-231 cell transcriptome in biological triplicate iCLIP experiments. RNA-seq was performed using three biological replicates of negative control siRNA treated MDA-MB-231 cells and three biological replicates of TRA2A and TRA2B siRNA treated MDA-MB-231 cells.
Contributor(s) Best A, James K, Dalgliesh C, Hong E, Kheirolahi-Kouhestani M, Curk T, Xu Y, Danilenko M, Hussain R, Keavney B, Wipat A, Klinck R, Cowell I, Lee KC, Austin C, Venables JP, Chabot B, Santibanez Koref M, Tyson-Capper A, Elliott DJ
Citation(s) 25208576
Submission date Jul 11, 2014
Last update date May 15, 2019
Contact name David J Elliott
Organization name Newcastle University
Department Institute of Genetic Medcine
Street address 1 Central parkway
City Newcastle upon Tyne
ZIP/Postal code NE1 3BZ
Country United Kingdom
Platforms (2)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (9)
GSM1435246 negative control siRNA treated MDA-MB-231 cells 1
GSM1435247 negative control siRNA treated MDA-MB-231 cells 2
GSM1435248 negative control siRNA treated MDA-MB-231 cells 3
BioProject PRJNA255099
SRA SRP044265

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Supplementary file Size Download File type/resource
GSE59335_count_on_ensembl71_exons.txt.gz 10.1 Mb (ftp)(http) TXT
GSE59335_exons_sig_anno_total.txt.gz 344.9 Kb (ftp)(http) TXT
GSE59335_peaks_id73602_rnd100_flank15_fdr0.05_regionAsOne_group_3317_Elliott1_sum_G_hg19--ensembl59_from_3297-3298-3299_bedGraph-cDNA-hits-in-genome.bed.gz_lowFDR.bed.gz 3.5 Mb (ftp)(http) BED
GSE59335_peaks_id73602_rnd100_flank15_fdr0.05_regionAsOne_group_3317_Elliott1_sum_G_hg19--ensembl59_from_3297-3298-3299_bedGraph-cDNA-hits-in-genome.bed.gz_lowFDR_clusters.bed.gz 932.8 Kb (ftp)(http) BED
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