|
| Status |
Public on Oct 23, 2017 |
| Title |
WT H3K4me2 ChIPseq-1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: WT
chip antibody: H3K4me2, 07-030 Millipore
cell type: MEF
strain: C57BL/6
|
| Treatment protocol |
Asynchronously growing cells were used for ChIP-seq.
|
| Growth protocol |
The cells were cultured in low glucose (1.0mg/L) Dulbecco-modified eagle's medium (DMEM) (Sigma) supplemented with 10% fetal bovine serum and antibiotics.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Crosslinked samples were fragmented using Covaris S220, followed by immunoprecipitation with the specific antibodies.
ChIP DNA was subjected to library preparation with NEBNext Fast DNA Library Prep Set for Ion Torrent kit (New England Biolabs.). DNA was end-repaired, adapter-ligated, and size-selected with Agentcourt AMpure XP (Beckman Coulter Inc.) to median length of 300bp. Size-selected DNA was PCR amplified with Ion barcode adapter (Thermo Fischer Inc.) for 12 cycles, and purified with Agentcourt AMpure XP. High-throughput sequencing was performed using Ion Proton semiconductors sequencers (Thermo Fischer Inc.) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
ChIP DNA and input controls were sequenced with the Ion Proton semiconducter sequencer.
WT_H3K4me2.bw
|
| Data processing |
Basecall was performed using Torrent Suite (Thermo Fischer Inc.)
Reads were aligned with mm9 genome using Bowtie2
The aligned reads with mapping quality score (MAPQ) >5 were used for peak detection.
Peak detection was performed with MACS v1.4.2 with default settings (p < 1*e-5).
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using MACS v1.4.2 with -w option.
|
| |
|
| Submission date |
Nov 21, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Yusuke Morita |
| E-mail(s) |
ysmorita@kuhp.kyoto-u.ac.jp
|
| Organization name |
kyoto university
|
| Street address |
kyoto
|
| City |
kyoto |
| State/province |
kyoto |
| ZIP/Postal code |
5360015 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18635 |
| Series (2) |
| GSE90107 |
Genome-wide analysis of Nrdc-binding sites by ChIP-seq in mouse embryonic fibroblasts |
| GSE90109 |
Nrdc-deficient MEF |
|
| Relations |
| BioSample |
SAMN06045283 |
| SRA |
SRX2364818 |
