|
| Status |
Public on Jan 14, 2023 |
| Title |
monkey spleen 6mA MeDIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
monkey spleen 6mA
|
| Organism |
Macaca mulatta |
| Characteristics |
strain: rhesus monkey
tissue: spleen
age: 3 years
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from Drosophila and other animal tissues using the Wizard genomic DNA purification Kit (Promega) following the manufacturer’s instructions. 5 µg of fragmented genomic DNA was immunoprecipitated with 5 µg of rabbit 6mA antibody (Abcam) or rabbit IgG overnight at 4°C in a final volume of 500 µl immunoprecipitation buffer. Then the mixture was incubated with 50 µl protein A/G agarose beads for 2 h at 4°C and then washed three times with 1 ml of immunoprecipitation buffer. The beads were then treated with proteinase K and the methylated DNA was purified by phenol-chloroform extraction followed by ethanol precipitation for library construction.
End repair, 3′-adenylation, adaptor ligation, and PCR amplification were performed according to Illumina TruSeq DNA sample preparation procedures. Libraries were sequenced using the Illumina Hiseq2500 V4 platform.
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
MeDIP-seq reads were aligned to the dm6 genome assembly using bowtie2 with with parameters “--no-mixed --no-discordant --non-deterministic --very-sensitive-local”
MACS2 callpeak was used to identify enrichment peaks with parameters “-f BAMPE –B” and a default q-value (FDR) cutoff of 0.05, and used IgG as a control
Genome_build: dm6
Supplementary_files_format_and_content: bed file of the callpeak result
|
| |
|
| Submission date |
Sep 09, 2016 |
| Last update date |
Jan 14, 2023 |
| Contact name |
Shunmin He |
| E-mail(s) |
hesm@ioz.ac.cn
|
| Phone |
010-64807279
|
| Organization name |
Institute of Zoology, Chinese Academy of Sciences
|
| Street address |
1 Beichen West Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL19129 |
| Series (1) |
| GSE90720 |
Fox Family Protein Jumu Reads 6mA-DNA Codes and Contributes to Zygotic Gene Activation |
|
| Relations |
| BioSample |
SAMN05762754 |
| SRA |
SRX2159565 |
| SRA |
SRX2409242 |
