|
Status |
Public on Dec 13, 2014 |
Title |
Sample_10_MeDIP |
Sample type |
SRA |
|
|
Source name |
Normal placentas tissue
|
Organism |
Homo sapiens |
Characteristics |
tissue: normal placenta antibody: anti-5mC antibody catalog/vendor: BI-MECY-1000, Eurogentec
|
Growth protocol |
Severely preeclamptic placentas and normal tissues were isolated from patients.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Genomic DNA of severely preeclamptic placentas and normal tissues was purified using the Qiagen Blood & Cell Culture DNA Mini Kit (Cat. No: 13323) and sonicated. Illumina barcode adapters were ligated before hMeDIP. Adaptor-ligated DNA (5 μg) was denatured and incubated with 3 μl of 5-hmC antibody (Active Motif) or 5 μg of 5-mC antibody (Eurogentec) at 4°C overnight. Antibody-DNA complexes were captured by protein A/G beads. The immunoprecipitated DNA was purified and sequenced following standard Illumina protocols. Libraries were prepared for sequencing using standard Illumina protocols
|
|
|
Library strategy |
MeDIP-Seq |
Library source |
genomic |
Library selection |
5-methylcytidine antibody |
Instrument model |
Illumina HiSeq 2500 |
|
|
Data processing |
base_calling: CASAVA package (Illumina v1.6) ChIP-seq reads were aligned to the hg19 genome assembly using bowtie-1.0.0 peaks were called using macs14 with the following setting:--pvalue=1e-5 Genome_build: hg19 Supplementary_files_format_and_content: bed and peak list,bg and Normalised density file
|
|
|
Submission date |
Dec 01, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Ruitu Lyu |
E-mail(s) |
lvruitu@gmail.com
|
Organization name |
Institutes of Biomedical Sciences Fudan University
|
Lab |
Epigenetics lab
|
Street address |
138 Yixueyuan Road Xuhui District
|
City |
Shanghai |
ZIP/Postal code |
200030 |
Country |
China |
|
|
Platform ID |
GPL16791 |
Series (1) |
GSE63743 |
Genome-Wide Mapping of 5-mC and 5-hmC in severely Preeclamptic Placentas. |
|
Relations |
BioSample |
SAMN03247134 |
SRA |
SRX791575 |