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| Status |
Public on Feb 28, 2020 |
| Title |
GM23916 Hi-C |
| Sample type |
SRA |
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| Source name |
lymphoblastoid cell
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| Organism |
Homo sapiens |
| Characteristics |
chromosomes: XO
cell line: GM23916
cell type: lymphoblastoid cell
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| Biomaterial provider |
Coriell; http://ccr.coriell.org/Sections/Search/Sample_Detail.aspx?Ref=GM23916
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lymphocytes were isolated from whole blood samples by centrifugation after dilution with PBS and underlaying Sigma Histopaque-1077 to the bottom. Genomic DNA and total RNA were extracted simultaneously from lymphocytes using QIAGEN's AllPrep DNA/RNA Mini Kit.
Five million cells were crosslinked with formaldehyde and lysed with protease inhibitors (Sigma, P8340). Chromatins were subsequently digested by MboI restriction enzyme (NEB, R0147). Restriction fragment overhangs were filled and the DNA ends were marked with biotin. Next, biotinylated DNA were sheared to a size of 300-500 bp, whose ends were repaired subsequently. dATP were attached and Illumina indexed adapter (TrueSeq nano) were ligated. The DNA fragments were then amplified and purified.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
In situ Hi-C data: Hi-C reads were mapped to reference genome (hg38) by BWA-MEM (version 0.7.7) in single end mode after ligation junction removal using Cutadapt (version 1.8.1). Uniquely mapped reads were paired up and filtered (e.g. duplicates, self-ligations, continuous genomic fragments or re-ligation events, regions with abnormally high concentrations in reads) using HOMER (version 4.8). Raw contact maps were constructed using HOMER 59 and corrected by total number of contacts for each sample.
Genome_build: hg38
Supplementary_files_format_and_content: [In situ Hi-C data] chromosome of read 1, position of read 1,strand of read 1, number of contacts, length of the read 1, chromosome of read 2, position of read 2,strand of read 2, length of the read 2. For "position of read", 0 is pos strand and 1 = neg strand.
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| Submission date |
Feb 18, 2019 |
| Last update date |
Feb 28, 2020 |
| Contact name |
Xianglong Zhang |
| Organization name |
Amgen Inc.
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| Department |
Department of Cardiometabolic Disorders
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| Street address |
One Amgen Center Dr.
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| City |
Thousand Oaks |
| State/province |
CA |
| ZIP/Postal code |
91320 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (1) |
| GSE126712 |
Comparative and integrated functional genomics analysis of Klinefelter and Turner syndromes reveals network-wide effects of the sex chromosome dosage changes |
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| Relations |
| BioSample |
SAMN10962717 |
| SRA |
SRX5388871 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3611747_TS_chrX.tags.tsv.gz |
95.2 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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