|
| Status |
Public on Dec 13, 2014 |
| Title |
Sample_7_hMeDIP |
| Sample type |
SRA |
| |
|
| Source name |
Severely preeclamptic placentas tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: severely preeclamptic placenta
antibody: anti-5hmC
antibody catalog/lot/vendor: 39769, 10310001, Active motif
|
| 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 |
SAMN03247125 |
| SRA |
SRX791562 |
