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Sample GSM2634300 Query DataSets for GSM2634300
Status Public on Aug 01, 2019
Title shSuv39h1 rep1
Sample type SRA
 
Source name mES
Organism Mus musculus
Characteristics cell type: embryonic stem cell
strain: J1
Treatment protocol total RNA were extracted using Trizol reagent and used for mRNA capture.
Growth protocol Mouse embryonic stem cells (mESCs, J1 strain) seeded on inactivated mouse embryonic fibroblast cells (MEF) feeder were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco#11995) supplemented with 10% fetal bovine serum (FBS, Gibco#16000-044), 1×non-essential amino acids (NEAA, Gibco#11140), 1×GlutaMAX-I (Gibco#35050-061), 7μM β-mercaptoethanol (Ameresco, Biotechnology grade, Cat#M8210), 10ng/ml mouse leukemia inhibitory factor (Millipore, Chemicon, Cat#LIF2050) and 1% antibiotic (Pen Strep, Gibco#15140-122). All mES cells were sub-passaged every 3-4 days by digesting the cell clone into single cell suspension using 0.25% Trypsin-EDTA (Gibco#25200072), and the resulted cells were divided on 3-5 fresh feeder-plates.
Extracted molecule total RNA
Extraction protocol A total amount of 2μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext®Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manual instructions and index codes were added to attribute sequences to each sample. RNA-seq libraries were prepared with TruSeq RNA Library Prep Kit v2 (Illumina) according to the manufacturer instruction, and were sequenced on an Illumina HiSeq X-10).
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimed for adaptor and low-quality sequence and then mapped to mm10 whole genome using tophat v2.0.13 with default parameters
Differences in expression were determined using Cuffdiff v2.2.1
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
 
Submission date May 22, 2017
Last update date Aug 01, 2019
Contact name Jin Sun
E-mail(s) sunjin@tongji.edu.cn
Organization name Tongji University
Department life science and technology
Lab Jiang
Street address siping1239
City shanghai
ZIP/Postal code 200092
Country China
 
Platform ID GPL21273
Series (2)
GSE99155 H3K36me3 protects the mouse epigenome from single nucleotide variations [mRNA-Seq]
GSE99156 H3K36me3 protects the mouse epigenome from single nucleotide variations
Relations
BioSample SAMN07151540
SRA SRX2840424

Supplementary file Size Download File type/resource
GSM2634300_shSuv39h1_rep1.txt.gz 143.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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