|
| Status |
Public on May 13, 2020 |
| Title |
sicontrol-2 |
| Sample type |
SRA |
| |
|
| Source name |
muscle
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
tissue: muscle
cell type: myotube
treatment: sicontrol
|
| Treatment protocol |
C2C12 cells were transfected with siRNAs against Hrp2/Dpf3a or control
|
| Growth protocol |
C2C12 cells were cultured in DMEM medium supplemented with 20% fetal bovine serum (FBS).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were resuspended in lysis buffer, centrifugated and resuspended for 60 min at 37℃ in Transposase reaction mix. The fragmented DNA was purified and added adaptor sequences by PCR. After DNA purification, DNA was sequenced on HiSeq X ten.
Construction of libraries were performed using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
ATAC-seq data were processed according to ENCODE Processing Pipeline.
Clean reads were mapped to Mus musculus genome (mm10) by Bowtie2 (version 2.2.6)
Regions of enrichments were called using the MACS2 (version 2.1.1) peak caller.
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 |
| GSE148296 |
HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN14558847 |
| SRA |
SRX8082235 |
