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Sample GSM1556604 Query DataSets for GSM1556604
Status Public on Dec 13, 2014
Title Sample_10_hMeDIP
Sample type SRA
 
Source name Normal placentas tissue
Organism Homo sapiens
Characteristics tissue: normal 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 SAMN03247124
SRA SRX791567

Supplementary file Size Download File type/resource
GSM1556604_Sample_10_hMeDIP_pool.fastq_RPKM.BedGraph.gz 74.9 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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