|
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.
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|
|
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
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|
|
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 |