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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 01, 2019 |
| Title |
H3.1WT H3K36me3 rep2 |
| Sample type |
SRA |
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| Source name |
mES
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| Organism |
Mus musculus |
| Characteristics |
cell type: embryonic stem cell
strain: J1
chip antibody: H3K36me3((Abclonal,Cat.#A2366, lot# 40648))
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| 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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
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| 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.
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| Submission date |
May 22, 2017 |
| Last update date |
Aug 01, 2019 |
| Contact name |
Jin Sun |
| E-mail(s) |
sunjin@tongji.edu.cn
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| Organization name |
Tongji University
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| Department |
life science and technology
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| Lab |
Jiang
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| Street address |
siping1239
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| City |
shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN07151549 |
| SRA |
SRX2840414 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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