|
| Status |
Public on Oct 02, 2017 |
| Title |
6mA-IP_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
peripheral blood mononuclear cell
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: peripheral blood mononuclear cell
antibody: m6A (N6-methyladenosine) (Synaptic Systems. Cat. No. 202 003)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using Qigen DNA Extract Kit (Cat#). Lysates were harvested from sonicated genomic DNA Immunoprecipitated with 6mA antibody
Libraries were constructed according to manufacturer’s instructions of NEB Next DNA library prep kit (EE7370L ). Briefly, Harvested DNA was ligated to adaptor using NEB Next DNA library prep kit. Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq X10 platform and 150bp paired-end reads were generated.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Base calling was performed using CASAVA version 1.8.2 (illumina)
DNA IP-seq reads were trimmed for adaptor sequence and mapped to human genome using BWA (v0.7.12) by default parameters.
Peaks were called using MACS2 (v2.1.1) with default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: wig files were generated using MACS2
|
| |
|
| Submission date |
Oct 02, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Minghui He |
| E-mail(s) |
hemh1320@qq.com
|
| Organization name |
Forevergen Biosciences Co., Ltd
|
| Department |
Bioinformatics Department
|
| Street address |
International Biotech Island
|
| City |
Guangzhou |
| ZIP/Postal code |
510030 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE104475 |
N6-Methyladenine DNA Modification in Human Genome |
|
| Relations |
| BioSample |
SAMN07728386 |
| SRA |
SRX3236437 |
