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| Status |
Public on Apr 01, 2014 |
| Title |
Twin26-1_FAIREseq |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Homo sapiens |
| Characteristics |
twin pairing: MZ twin pair 26 sibling 1
tissue: blood
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were cross-linked by treating formaldehyde 1% for 5 min at room temperature followed by addition of 125mM glycine for 5 min and spinning at 3600g for 5 min. Pellets were washed three times with phosphate buffered saline and quickly frozen in liquid nitrogen. Subsequently, pellets were resuspended by adding 1ml lysis buffer (1% Triton X-100, 140 mM NaCl, 50mM HEPES-KOH at pH7.5, 0.1% Sodium Deoxycholate, 1 mM EDTA buffer) and disrupted by five cycles of 1-min vortexing and 2-min resting using glass beads (Sigma). Afterward, samples were sonicated for 60 rounds of 30 sec ON and 60 sec OFF using Bioruptor sonicator (Diagenode) and debris was cleared by centrifugation at 13000g for 10 min at 4°C. Finally, nucleosome-depleted DNA was extracted with phenol-chloroform followed by ethanol precipitation and RNase A (100 μg/ml) treatment.
After ensuring that the majority of DNA fragments were in the 100–350 bp range, 50-bp single-end Illumina HiSeq2000 sequencing was performed.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
FAIRE-seq
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| Data processing |
Raw data processing was carried out by means of Illumina data pipeline (ELAND and CASAVA). To identify the peaks of the reads, we ran Zinba with the default parameters. Meta-peaks were generated by merging the 72 FAIRE peak regions by using BEDTools.
Genome_build: hg19
Supplementary_files_format_and_content: bed
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| Submission date |
Apr 01, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Hyo-Jeong Ban |
| E-mail(s) |
hj.ban81@gmail.com
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| Organization name |
KCDC
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| Department |
bioinformatics
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| Street address |
OHTAC, Yeonje-ree 643, Osong-eup, Chungwon-Koon
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| City |
Choongchung-Buk-do |
| ZIP/Postal code |
363-951 |
| Country |
South Korea |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE44742 |
Genetic differences underlying chromatin discordance between monozygotic twins [FAIR-seq] |
| GSE53823 |
Genetic differences underlying chromatin discordance between monozygotic twins |
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| Relations |
| BioSample |
SAMN02714066 |
| SRA |
SRX506434 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1361329_Twin26-1.bed.gz |
1.3 Gb |
(ftp)(http) |
BED |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
| Raw data are available in SRA |
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