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| Status |
Public on Aug 08, 2016 |
| Title |
TOF-08 TOF |
| Sample type |
SRA |
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| Source name |
right ventricle
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| Organism |
Homo sapiens |
| Characteristics |
tissue: heart
disease state: Tetralogy of Fallot
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA from cardiac samples was extracted using Phenol:Chloroform:Isoamyl Alcohol (25:24:1) and treated with RNase A (Invitrogen) according to manufacturer’s instructions. DNA fragmentation was performed on a Covaris S3 to obtain fragments with an average length of 200 bp. The fragment distribution was examined on a high sensitivity DNA chip. Methylated DNA was captured using the MethylCap kit (Diagenode AF-100-0048, Belgium). The concentrations of the fragmented and captured DNA were determined on a Fluostar Optima plate reader (BMG Labtech, Offenburg, Germany) with the Quant-iTTN Picogreen dsDNA assay kit (Invitrogen P7589, Merelbeke, Belgium).
Library preparation and amplification were performed according to the ‘multiplexed paired-end ChIP protocol’ (with modifications) including the indexes from the ‘Multiplexing Sample Preparation Oligo Kit’ (Illumina, San Diego, California, USA). The libraries were 2 x 51 bp paired-end sequenced on an Illumina HiSeq 2000 platform. Base calling was performed with the Illumina Casava pipeline version 1.8.0. Initial sequencing quality assessment was based on data passing the Illumina Chastity filter.
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| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
TOF
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| Data processing |
base calling using Illumina Casava pipeline 1.8.0
read mapping using Bowtie v0.12.7 (zero mismatches in the first 28 nucleotides; only unique paired reads were retained and both fragments must be located within 400 bp of each other on the reference genome)
calculating methylation score for each CpG site using BALM v1.0.1 (enrichment level of 0.99)
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: tab separated text file with the chromosome number, coordinate and CpG methylation score (between 0 and 1)
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| Submission date |
Oct 22, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Silke Sperling |
| E-mail(s) |
silke.sperling@charite.de
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| Phone |
++49 (0)30 450540123
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| Organization name |
Experimental and Clinical Research Center (ECRC), Charité / MDC for Molecular Medicine
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| Department |
Cardiovascular Genetics
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| Lab |
Cardiovascular Genetics
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| Street address |
Lindenberger Weg 80
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| City |
Berlin |
| State/province |
Berlin |
| ZIP/Postal code |
13125 |
| Country |
Germany |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE62629 |
Comparative DNA methylation and gene expression analysis identifies novel genes for structural congenital heart diseases |
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| Relations |
| BioSample |
SAMN03135761 |
| SRA |
SRX738934 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1530474_TOF-08_rv_BALM_CpGscore.txt.gz |
176.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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