|
| Status |
Public on Apr 07, 2024 |
| Title |
FGSC_5mc_200_cells_super_cMeDIP-seq_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
FGSC
|
| Organism |
Mus musculus |
| Characteristics |
sample type: FGSCs
|
| Growth protocol |
FGSCs cultured on gelatinized plates with minimum essential medium (MEM)-α containing 10 % fetal bovine serum and several growth factors as in our previous report [Zhang et al. Genome Biology 2016]
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was harvested using AllPrep DNA/RNA Mini Kit (Qiagen) and sonicated with a sonicator and MeDIP DNA was isolated with antibody.
Libraries were prepared as super cChIP-seq or super cMeDIP-seq protocol described.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
super_cMeDIP-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 |
GPL13112 |
| Series (1) |
| GSE136578 |
Super cChIP-seq, a robust and universal epigenetic profiling method using 10 cells |
|
| Relations |
| BioSample |
SAMN12648169 |
| SRA |
SRX6767279 |
