Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 21
Release date: Oct 29 2016
Last update date: Nov 21 2018
Access: Public
Diseases: Cleft Palate
Dataset link The RNA-binding landscape of RBM10 and its role in alternative splicing regulation in models of mouse early development

Experimental Protocol


We carried out the iCLIP-seq of endogenous mouse RBM10 protein in 4 independent replicates in a mouse mandibular MEPA (Mouse Embryonic Pharyngeal Arch) cell line. For each replicate, we included a control iCLIP corresponding to an IP with rabbit IgG. Reads were mapped to the mouse genome (mm9) and we deduced the crosslink nucleotide counts for each genomic position. We performed RNA-Seq on polyA+ RNA isolated from RBM10 Knockout in md MEPA and ES cells. RBM10 KO md MEPA cells were obtained using CRIPR/Cas9 approach. We extracted RNAs from 4 independent RBM10 KO md cell lines (KO1 and KO2 with deletion in exon 3 and KO3 and KO4 with deletion in exon 9) and from WT md MEPA cells (Cont) in triplicates. RBM10 KO ES cell line, that correspond to the male gene trap cell line Rbm10Gt(CSI176)Byg, was obtained from Baygenomics. We also obtained the parental cell line E14Tg2a.4 from Baygenomics. RNAs were extracted from RBM10 KO and Cont ES cells in triplicates.

Repositories


GEO

GSE89270

ENA

SRP092246

BioProject

PRJNA351215

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