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Series GSE52856 Query DataSets for GSE52856
Status Public on Dec 02, 2014
Title Gene Expression and Exon Splicing Change Analysis of Mouse N2A Cell Transcriptome upon Polypyrimidine tract-binding protein depletion (II)
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Splicing factors regulate splice site choices in pre-mRNA and determine final exon set in mRNA. To understand mechanisms of splicing regulation, it is important to identify and characterize exon targets of splicing factors. Recently, development of RNA-seq technology enables researchers to investigate exon splicing profiles as well as gene expression profiles in transcriptome-wide. The goal of this study is to investigate transcriptome changes by splicing factors, Polypyrimidine Tract Binding proteins (PTB). In this study, we analyzed exon and gene expression changes followed by Ptbp1, Ptbp2, and both Ptbp1 & Ptbp2 knock down.
Methods: The knockdown experiment was performed in mouse neuroblastoma (N2A) cells. Total RNA was collected from cells and further treated with DNase I to avoid DNA contamination. RNA-seq libraries were constructed in a strand specific way using dUTP and Uracil-Specific Excision Reagent enzyme. The libraries were subjected to 100bp paired-end sequencing (Illumina HiSeq2000 platform).
 
Overall design Poly(A)-mRNA and exon profiles of N2A mouse blastoma cells in four samples: shRNA transfection control, single knock down of ptbp1, single knock down of ptbp2, double knock down of ptbp1 and ptbp2. RNA-seq libraries were generated in strand specific way using dUTP and USER enzyme and sequenced using Illumina HiSeq2000.
 
Contributor(s) Han A
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BioProject PRJNA192958
Submission date Dec 02, 2013
Last update date May 15, 2019
Contact name Areum Han
E-mail(s) arhan@ucla.edu
Organization name UCLA
Lab Black lab
Street address 6577 MacDonald Research Lab. 675 Charles E. Young Dr. South
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platforms (1)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
Samples (4)
GSM1097468 ptbp2kd (Sample 3)
GSM1097469 ptbp1ptbp2kd (Sample 4)
GSM1277104 control (Sample 1)
Relations
SRA SRP033517

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

Supplementary file Size Download File type/resource
GSE52856_RAW.tar 1.2 Gb (http)(custom) TAR (of BW, GTF, TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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