|
| Status |
Public on Apr 07, 2024 |
| Title |
K562_H3K4me3_1K_cells_super_cChIP-seq_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
sample type: K562 cells
|
| Growth protocol |
K562 cells were cultured in RPMI-1640 medium supplemented with 10% fetal calf serum (FCS) and Penicillin-Streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin DNA was sonicated and ChIP DNA was enriched with antibody.
Libraries were prepared as super cChIP-seq or super cMeDIP-seq protocol described.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
super_cChIP-seq
|
| Data processing |
Raw reads were trimmed using Trimmomatic (version 0.38)
Bowtie (version 1.2.2) was used to align the clean reads to the reference genome (hg19 for human and mm10 for mouse).
The uniquely mapped reads after the removal of duplicates were used for the downstream analysis
Peaks were obtained using MACS (version 2.1.1) with corresponding input samples.
Genome_build: hg19 or mm10
Supplementary_files_format_and_content: The bigwig files were generated with the function bamCoverage from DeepTools27 using with the following parameters (--binSize 200 and --smoothLength 1,000), and binSize 1,000 was used when processing MeDIP data
|
| |
|
| Submission date |
Aug 28, 2019 |
| Last update date |
Apr 07, 2024 |
| Contact name |
Xiaodong Zhao |
| E-mail(s) |
congxiahu0606@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Lab |
zxd lab
|
| Street address |
800 Dongchuan RD
|
| City |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE136578 |
Super cChIP-seq, a robust and universal epigenetic profiling method using 10 cells |
|
| Relations |
| BioSample |
SAMN12648157 |
| SRA |
SRX6767255 |
