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Sample GSM1631190 Query DataSets for GSM1631190
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.
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.
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
BioSample SAMN03397416
SRA SRX950719

Supplementary file Size Download File type/resource
GSM1631190_mESC_RNAseq_shTex10-rep1.fpkm.tsv.gz 581.7 Kb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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