|
Status |
Public on May 06, 2015 |
Title |
mESC_RNAseq_shTex10-rep1 |
Sample type |
SRA |
|
|
Source name |
Embryonic stem cells
|
Organism |
Mus musculus |
Characteristics |
cell line: CCE strain: 129SV knockdown: shTex10
|
Treatment protocol |
CCE mESCs were treated with control luciferase depletion (shLuci) or Tex10 depletion (shTex10) shRNAs
|
Growth protocol |
mESCs were grown in DMEM (GIBCO) supplemented with 15% Serum (Corning), 10^3 units/ml recombinant murine Leukemia Inhibitory Factor (LIF) (ESGRO, Millipore), 2mM L- alanyl-L-glutamine dipeptide (Glutamax; Invitrogen), 1x non-essential amino acids (Invitrogen), and 0.1mM 2-mercaptoethanol (Sigma). mESCs were passaged every two day as a single cell suspension using 0.05% trypsin/EDTA and seeded at 3.0x10^4 cells/cm^2 for routine culture. All cells were grown on 0.1% (w/v) gelatin coated tissue culture dish.
|
Extracted molecule |
polyA RNA |
Extraction protocol |
RNA was extracted from ~2x10^6 cells with TRIzol (Invitrogen), separated using Phase Lock Gel tubes (5 Prime), and purified using the RNAeasy Plus kit (Qiagen) according to the manufacturer’s protocol. PolyA+ RNA was prepared for sequencing using the Illumina TruSeq RNA Sample Preparation Kit according to the manufacturer's protocol. We prepared 20 µl of 100 ng/µl total RNA for each sample to do massively parallel sequencing with the Illumina HiSeq 2500, followed by the manufactory instructions, with a poly-A selection protocol. 100-bp single end reads were generated for each sample.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
Reads were aligned to the genome using TopHat (v2.0.10) and Bowtie2 (v2.1.0) with the default parameter settings. Transcript assembly and differential expression analysis were performed using Cufflinks (v2.1.1). Assembling of novel transcripts was not allowed (-G), other parameters of Cufflinks followed the default setting. Genome_build: mm9 Supplementary_files_format_and_content: tsv files - tab-delimited files containing FPKM values for RefSeq genes in each sample generated using Cufflinks.
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|
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Submission date |
Mar 10, 2015 |
Last update date |
May 15, 2019 |
Contact name |
Jianlong Wang |
Organization name |
Columbia University Irving Medical Center
|
Department |
Department of Medicine
|
Lab |
Jianlong Wang
|
Street address |
650 W. 168th St.
|
City |
New York |
State/province |
New York |
ZIP/Postal code |
10032 |
Country |
USA |
|
|
Platform ID |
GPL17021 |
Series (2) |
GSE66734 |
Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity for Pluripotency and Reprogramming [RNA-Seq] |
GSE66736 |
Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity for Pluripotency and Reprogramming |
|
Relations |
BioSample |
SAMN03397416 |
SRA |
SRX950719 |