|
| Status |
Public on Aug 23, 2020 |
| Title |
Ssrp1 KO Usp7 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic stem cell
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129/Ola
genotype: Ssrp1 KO
cell line: E14 embryonic stem cells (ESCs)
chip antibody: Anti-Usp7 (Bethyl A300-033A)
|
| Treatment protocol |
Mouse E14 embryonic stem cells
|
| Growth protocol |
Mouse E14 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin(Sigma),in medium(Hyclone) that supplement with 15% FBS（Hyclone）,10ng/ml mLIF (GenScript)，1% Penicillin-Streptomycin (Solarbio)，1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed and chromatin was extracted. Anti-Ssrp1 antibody was used to immunoprecipiate Ssrp1 in mESCs. And Anti-Usp7 antibody was used to immunoprecipiate Usp7 in WT and Ssrp1 KO mESCs. Proteins on chromatin associated with Ssrp1 was digested and chromatin was decrosslinked at 65 degree overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Ssrp1-assocated chromatin DNA was used in ChIP-seq library preparation. Libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
Ssrp1_KO_Usp7.bw
|
| 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.
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 05, 2020 |
| Last update date |
Aug 23, 2020 |
| Contact name |
Weiyu Zhang |
| E-mail(s) |
[email protected]
|
| 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 (1) |
| GSE141791 |
ChIP-seq analysis of Ssrp1 and Usp7 in mESCs |
|
| Relations |
| BioSample |
SAMN15738126 |
| SRA |
SRX8893872 |
