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Sample GSM3560408 Query DataSets for GSM3560408
Status Public on May 07, 2019
Title HiC_wbc_rep2
Sample type SRA
 
Source name white blood cells
Organism Homo sapiens
Characteristics cell type: primary cell
restriction enzyme: Arima (multi-enzyme)
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.
 
Library strategy Hi-C
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
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.
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
 
Submission date Jan 11, 2019
Last update date May 09, 2019
Contact name Yaping Liu
E-mail(s) lyping1986@gmail.com
Organization name Cincinnati Children's Hospital Medical Center
Department Department of Pediatrics
Lab EpiFluid Lab in Division of Human Genetics
Street address 3333 Burnet Ave
City Cincinnati
State/province OH
ZIP/Postal code 45229
Country USA
 
Platform ID GPL20795
Series (1)
GSE124974 Spatial co-fragmentation pattern of cell-free DNA recapitulates in vivo chromatin organization and identifies tissue-of-origin
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 SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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