|
| Status |
Public on Jun 01, 2019 |
| Title |
ATAC-seq ES KO re1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Trim33 null
strain: C57Bl/6J background ESCs(Xi et al., 2011)
cell type: embryonic stem cell
|
| Treatment protocol |
Trim33 null ESCs in C57Bl/6J background were cultured on galetin coated plates with LIF-supplemented medium
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 |
Trim33 null ESCs in C57Bl/6J background were cultured on galetin coated plates with LIF-supplemented and 15% serum medium
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 |
After dissociation with Trypsin, embryonic stem cells were washed with PBS and incubated in lysis buffer.
ATAC-Seq libraries were prepared using ATAC-seq developed by Buenrostro et al. with slightly modification
After scraped from plate, embryonic stem cells were washed with PBS and incubated in lysis buffer.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| 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
|
| |
|
| 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 |
SAMN09289131 |
| SRA |
SRX4147799 |
