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| Status |
Public on May 07, 2019 |
| Title |
HiC_wbc_rep2 |
| Sample type |
SRA |
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| Source name |
white blood cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: primary cell
restriction enzyme: Arima (multi-enzyme)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
WBCs are freshly isolated from whole blood, purified neutrophils are obtained frozen from a commercial source (Astarte Biologics Inc) and then thawed
Hi-C library preparation on white blood cells and neutrophils was performed using the Arima-HiC kit (Arima Genomics, Inc.; Cat # A510008), according to the manufacturer’s protocols. Briefly, WBCs (freshly isolated from whole blood) or purified neutrophils (obtained frozen from a commercial source and then thawed) were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using SPRI beads. The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. The purified, PCR-amplified DNA underwent standard QC (qPCR and Bioanalyzer) and was sequenced with unique dual indexes on the Illumina HiSeq X (WBC) or NovaSeq 6000 (neutrophils) Sequencing System at 2x151 base pairs.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
Hi-C library preparation on white blood cells and neutrophils was performed using the Arima-HiC kit (Arima Genomics, Inc.; Cat # A510008), according to the manufacturer’s protocols. Briefly, WBCs (freshly isolated from whole blood) or purified neutrophils (obtained frozen from a commercial source and then thawed) were crosslinked using formaldehyde. Crosslinked cells were then subject to the Arima-HiC protocol, which utilizes multiple restriction enzymes to digest chromatin. Arima-HiC sequencing libraries were prepared by first shearing purified proximally-ligated DNA and then size-selecting 200-600 bp DNA fragments using SPRI beads. The size-selected fragments were then enriched using Enrichment Beads (provided in Arima-HiC kit), and then converted into Illumina-compatible sequencing libraries with TruSeq adapters using the KAPA Hyper Prep kit. The purified, PCR-amplified DNA underwent standard QC (qPCR and Bioanalyzer) and was sequenced with unique dual indexes on the Illumina HiSeq X (WBC) or NovaSeq 6000 (neutrophils) Sequencing System at 2x151 base pairs.
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| Data processing |
Hi-C data processing: Raw fastq files from various Hi-C experiments were uniformly processed using Juicer command line tools v1.5.6 and aligned to the human genome (GRCh38 with decoys, alt contigs, and HLA contigs). Only results after filtering reads with mapping quality score > 30 were used to generate a Pearson correlation matrix and compartment A/B eigenvector. PCA was performed using the PCA function in scikit-learn 0.19.1 in Python 3.6. The first principal component was used to segment the compartments. For each chromosome, compartments were split into two groups based on their sign. After excluding regions with mappability less than 0.75, the group of compartments with the lower mean gene density (based on Ensembl v84 annotations) was defined as compartment B; the other group was defined as compartment A. HiCCUPS loops were called by hiccups command line in Juicer with parameters “-k KR -m 512 -r 5000,10000,25000 -f .1,.1,.1 -p 4,2,1 -i 7,5,3 -t 0.02,1.5,1.75,2 -d 20000,20000,50000”.
Genome_build: hg38
Supplementary_files_format_and_content: hic
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| Submission date |
Jan 11, 2019 |
| Last update date |
May 09, 2019 |
| Contact name |
Yaping Liu |
| E-mail(s) |
lyping1986@gmail.com
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| Organization name |
Northwestern University
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| Department |
Department of Biochemistry and Molecular Genetics
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| Lab |
EpiFluid Lab
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| Street address |
303 E Superior St
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| City |
Chicagp |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE124974 |
Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissue-of-origin |
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| Relations |
| BioSample |
SAMN10734076 |
| SRA |
SRX5242867 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3560408_WBC_rep2.hg38.hic |
1.4 Gb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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