|
| Status |
Public on Jun 01, 2019 |
| Title |
H3K27ac ChIP-seq EB AC |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
treatment: activin A (50 ng/ml, R&D Systems)
genotype/variation: wild type
strain: E14
cell type: d2.5 EBs
antibody: H3K27ac
|
| Treatment protocol |
differentiatino was induced on ultra-low plates with medium withdraw LIF and cells were harvested at d2.5 before activin A (50 ng/ml, R&D Systems) treated for 2hs
Embryoid body (EB) formation and differentiation were carried out as described by the supplier (ATCC). Prior to total RNA extraction cells were treated with activin A (50 ng/ml, R&D Systems) or SB431542 (10 mM, TOCRIS).
|
| Growth protocol |
E14 WT ESCs were induced into differentiation on ultra-low plates with 15% serum medium withdraw LIF and cells were harvested at d2.5 before activin A (50 ng/ml, R&D Systems) treated for 2hs
mESCs were maintained on gelatin-coated plates with ESCs culture serum medium as descriped in Wang et al.2017
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked with 1% formaldehyde at 37 °C for 10 min and quenched with 0.125 M glycine for 5 min at room temperature. Then cells were scraped and ChIP was performed and DNA were extracted using a ChIP assay kit (Millipore) as described.
For library construction and sequencing, ChIP-Seq DNA samples were quantified and quality assessed by Qubit 2.0 and Agilent 2100. DNA fragments range from 200-600bp were selected constructed for ChIP-Seq library with TruSeq ChIP Sample Prep Kit (Illumina) according to manufacturer’s instructions.
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
ATAC-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
RNA-Seq reads were aligned to the mm9 genome assembly using STAR version 2.4.0, then replicates were merged together, and transcript abundance (FPKM) were calculated based on Refseq annotation using cufflinks version 2.2.1
ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9
Supplementary_files_format_and_content: The wig files counted by the number of reads falling into 100bp bin in the genome. Tab-delimited text files include RPKM values for each sample
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| |
|
| Submission date |
May 31, 2018 |
| Last update date |
Jun 01, 2019 |
| Contact name |
Bofeng Liu |
| E-mail(s) |
lbf12thu@gmail.com
|
| Organization name |
Tsinghua University
|
| Department |
School of Life Science
|
| Lab |
Xie Wei Lab
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE115169 |
Nodal signaling maintains H3K18ac landscape to promote mesendodermal differentiation through TRIM33 |
|
| Relations |
| BioSample |
SAMN09289144 |
| SRA |
SRX4147809 |
