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Sample GSM2634288 Query DataSets for GSM2634288
Status Public on Aug 01, 2019
Title H3.1WT input rep1
Sample type SRA
 
Source name mES
Organism Mus musculus
Characteristics cell type: embryonic stem cell
strain: J1
chip antibody: none
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 genomic DNA
Extraction protocol Chromatin of cross-linked mESCs with H3.1WT overexpressing were sonicated into near 500bp length, the chromatin solution were captured by 2ug of rabbit polyclonal anti-H3K36me3 antibody (Abclonal, Cat.#A2366, lot# 40648)
The ChIP DNAs were measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific). The libraries were prepared using NEBNext Ultra™ DNA Library Prep Kit for Illumina (NEB, #E7370) according to the manual instruction.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model HiSeq X Ten
 
Data processing Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the mm10 genome assembly using Bowtie version 2.0.0-beta6 with parameters -D 15 -R 2 -N 0 -L 32 -i S,1,0.75 -M 10000
Reads aligned to mitochondrial genome and unassigned sequences were removed. Reads overlap the blacklist regions generated by ENCODE project were also removed.
Then the ChIP-seq were transformed into read coverage files normalized to 1x sequencing depth at 10 bp resolution and minus input file using deepTools package(http://deeptools.github.io).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig ChIP minus Input file. Signal value represent the ChIP-seq normalized read coverage minus the input normalized read coverage.
 
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)
GSE99154 H3K36me3 protects the mouse epigenome from single nucleotide variations [ChIP-Seq]
GSE99156 H3K36me3 protects the mouse epigenome from single nucleotide variations
Relations
BioSample SAMN07151536
SRA SRX2840411

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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