|
| Status |
Public on May 13, 2020 |
| Title |
MT-siHRP2-HRP2-input |
| Sample type |
SRA |
| |
|
| Source name |
muscle
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
tissue: muscle
cell type: myotube
chip antibody: none
|
| Growth protocol |
C2C12 cells were cultured in DMEM medium supplemented with 20% fetal bovine serum (FBS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For TY1,HRP2 and DPF3a ChIP, cells were double cross-linked with DMA and 1% formaldehyde. For H3K36me2 ChIP, cells were cross-linked with 1% formaldehyde. The crosslink was stopped by adding 2.5 M glycine. Cells were washed with PBS and harvested using ChIP lysis buffer. Cells were then sonicated to obtain fragments (100-500 bp) with Bioruptor Sonicator. Immunoprecipitation was performed withTY1, HRP2 (15134-1-AP), DPF3a and H3K36me2 (ab9049). After elution and reversal cross-linking, DNA was purified and sequenced on HiSeq X ten.
Construction of ChIP-seq library was performed using VAHTSTM Universal DNA Library Prep Kit for Illumina® V3 (Vazyme).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
ChIP-seq data were processed according to ENCODE Processing Pipeline.
Clean reads were mapped to Mus musculus genome (mm10) by BWA (version 0.7.13)
Peaks were called using peak finding algorithm MACS2 (version 2.1.1)
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated by deeptools
|
| |
|
| Submission date |
Apr 08, 2020 |
| Last update date |
May 14, 2020 |
| Contact name |
Bingxue Lan |
| Organization name |
Tianjin Medical University
|
| Street address |
Qixiangtai road
|
| City |
Tianjin |
| ZIP/Postal code |
300070 |
| Country |
China |
| |
|
| Platform ID |
GPL21273 |
| Series (2) |
| GSE141407 |
HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription |
| GSE148295 |
HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription [ChIP-Seq] |
|
| Relations |
| BioSample |
SAMN14558857 |
| SRA |
SRX8082202 |
