|
| Status |
Public on Jun 30, 2023 |
| Title |
Zscan4 OE ESC IP of H3K9me3 |
| Sample type |
SRA |
| |
|
| Source name |
J1
|
| Organism |
Mus musculus |
| Characteristics |
strain: 12910la
cell line: J1
cell type: Embryonic stem cell
genotype: Zscan4 overexpression
chip antibody: H3K9me3
|
| Treatment protocol |
The CDS region of Zscan4c was cloned into pCMV-FLAG vector.WT mESCs were transfected with 1000ng pCMV-tag2 vector.After transfection for 24h,the cells were treated with 500ug/ml G418 for 10days and the medium were changed every 24h，then we picked monoclonal cells.
|
| Growth protocol |
Mouse J1 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 with15% FBS（Hyclone）,10ng/ml mLIF (GeneScript)，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-H3K9me3 antibodies were used to immunoprecipiate FLAG-Zscan4 in mESCs. Proteins on chromatin associated with Zscan4 was digested and chromatin was decrosslinked at 65 degree overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Zscan4-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 |
OE_H3K9me3_H3K9me3_mm10.bw
|
| Data processing |
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutdadpt, 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 |
Jul 13, 2021 |
| Last update date |
Jun 30, 2023 |
| Contact name |
Xuan Zhao |
| E-mail(s) |
2120191260@mail.nankai.edu.cn
|
| Phone |
13780330130
|
| Organization name |
Nankai University
|
| Department |
State Key Laboratory of Medicinal Chemical Biology
|
| Lab |
XinyiLu-Lab
|
| Street address |
No. 38 Tongyan Road, Haihe Education Park, Tianjin
|
| City |
Tianjin |
| State/province |
Tianjin |
| ZIP/Postal code |
300000 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (1) |
| GSE180003 |
CHIP-seq analysis about H3K9me3 change after Zscan4 overexpression |
|
| Relations |
| BioSample |
SAMN20197335 |
| SRA |
SRX11430310 |
