|
| Status |
Public on May 29, 2018 |
| Title |
EpiSCS/F-H3K27me3-ChIP seq |
| Sample type |
SRA |
| |
|
| Source name |
EpiSCS/F-H3K27me3
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Epiblast stem cells cultured in Nodal inhibited medium
chip antibody: H3K27me3 (Millipore,07-449)
|
| Growth protocol |
EpiSCs were maintained on serum-coated plates in chemical defined medium (CDM) supplemented with Activin (20ng/ml) and bFGF (10ng/ml). To derive EpiSCsS/F, EpiSCs were dissociated as small clumps with collagenase IV and replated on serum-coated plates in CDM supplemented with 2μM SB431542 and bFGF (10ng/ml). EpiSCsS/F were passaged using collagenase IV every 2 days. EpiSCsS/F can be cryopreserved using KSR plus 10% DMSO (dimethylsulfoxide) and thawed with similar viability compared with EpiSC.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected and fixed in 1% formaldehyde solution and quenched by 0.125M glycine. Fixed cells were fragmented to a size range of 200-500bp by using Bioruptor Pico. Solubilized fragmented chromatin was immunoprecipitated with antibodies.Fragmented DNA was extracted with phenol-chloroform and precipitated with ethanol
DNA fragments acquired from immunoprecipitation would be subjected to end-repaired, adaptor ligation and PCR amplification under the instruction of the manufacturers (New England Biolabs E7370 ).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw reads were mapped to mm10 using Bowtie2 version 2.2.2 program
MACS2 version 2.1.1.20160309 was used to call ChIP-seq peaks using broad peak calling mode (with --broad option), as well as to identify differential ChIP-seq signals in different conditions
ChIPseeker was used to annotate ChIP-seq peaks by using the mouse gene annotation GENCODE version M9
deepTools was used to smooth and calculate the ChIP-seq signal as the ratio between ChIP-seq data and corresponding input control data, as well as to visualize ChIP-seq signals.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Dec 20, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Naihe Jing |
| E-mail(s) |
njing@sibcb.ac.cn
|
| Organization name |
Shanghai Institute of Biochemistry and Cell Biology
|
| Street address |
Yue Yang Road 320
|
| City |
Shanghai |
| ZIP/Postal code |
200031 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE92633 |
Genome-wide maps of chromatin state in epiblast stem cells and nodal inhibited ebiblast stem cells |
| GSE92635 |
Suppressing Nodal Signaling Activity Predisposes Ectodermal Differentiation of Epiblast Stem Cells |
|
| Relations |
| BioSample |
SAMN06167372 |
| SRA |
SRX2437257 |
