|
| Status |
Public on Aug 22, 2020 |
| Title |
bulk Primed H3K9me3 replicate |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57 x CBA
cell type: Embryonic stem cell
condition: primed
passage: 15
chip anitbody: H3K9me3 abcam ab176916
|
| Treatment protocol |
For ULI-NChIP-seq, about 50000 naïve or primed cells were used per reaction. For bulk ChIP-seq, about 5000000 naïve or primed cells were used per reaction.
|
| Growth protocol |
Naive cells were cultured in serum+LIF condition on feeders, primed cells were cultured in bFGF+Activin A condition on feeders.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ULI-NChIP procedure was performed as previously described(Brind'Amour et al., 2015; Wang et al., 2018).
Sequencing libraries were generated using AT seq library following manufacturer's recommendations and index codes were added. The library quality was assessed on the Qubit 2.0 Fluorometer (Thermo Scientific) and Agilent Bioanalyzer 2100 system. At last, the library was sequenced on an Illumina HiSeq x platform and 150 bp paired-end reads were generated
Ultra-low-input micrococcal nuclease-based native ChIP (ULI-NChIP)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt, then sequence reads were mapped to mm10 genome using Bowtie2.
The aligment files of bulk ChIP-seq and micro ChIP-seq were merge together, and Bigwig file was generated by bamCompare from Deeptools
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files, ChIP-seq normalized signal
|
| |
|
| Submission date |
Aug 09, 2020 |
| Last update date |
Oct 19, 2020 |
| Contact name |
Weiyu Zhang |
| E-mail(s) |
ch8316f5eyu@gmail.com
|
| Phone |
18902012072
|
| Organization name |
Nankai University
|
| Street address |
No.38 Tongyan Road, Jinnan District
|
| City |
Tainjin |
| ZIP/Postal code |
300350 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE140667 |
Regulation of retrotransposon activity and telomeres in primed pluripotent stem cells |
| GSE154487 |
Regulation of retrotransposon activity and telomeres in primed pluripotent stem cells (ChIP-seq) |
|
| Relations |
| BioSample |
SAMN15769456 |
| SRA |
SRX8913627 |
