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Sample GSM6459718

Query DataSets for GSM6459718

Status

Public on Sep 07, 2022

Title

Capture Hi-C, NA07000-batch-3, biological replicate A

Sample type

SRA

Source name

Epstein-Barr Virus- (EBV-) Immortalized Lymphoblastoid Cell Line (LCL)

Organism

Homo sapiens

Characteristics

tissue: Epstein-Barr Virus- (EBV-) Immortalized Lymphoblastoid Cell Line (LCL)
cell line: NA07000 LCL
cell type: B-cell derived LCL
genotype: NA07000
treatment: none

Growth protocol

LCLs were maintained in RPMI medium supplemented with 10% FBS and 1% penicillin-streptomycin, and were grown at 37C in 5% CO2.

Extracted molecule

genomic DNA

Extraction protocol

Capture Hi-C libraries were prepared according to the protocol described in (Jäger et al., 2015: PMID: 25695508). The protocol consists of two parts: Hi-C library preparation and target enrichment (Figure 1A). A SureSelect Custom Target Enrichment Library covering a 3Mb region in the 8p23.1 (hg19 coordinates: chr8:8190000-11838000) was designed using eArray software (Agilent). Hi-C library preparation, comprising chromatin fixation, HindIII digestion, biotin labelling, ligation and crosslink reversal was performed as described in (Rao et al., 2014: PMID: 25497547) with minor modifications described in (Jäger et al., 2015). Target enrichment was performed according to the SureSelect protocol (Agilent) with minor modifications described in (Jäger et al., 2015: PMID: 25695508). We have prepared 10 capture Hi-C libraries from 5 independent batches of NA07000 cells and 4 capture Hi-C libraries from 2 independent batches of NA07056 cells (2 biological replicates per cell batch).
Capture Hi-C

Library strategy

OTHER

Library source

genomic

Library selection

other

Instrument model

Illumina HiSeq 2500

Data processing

The capture Hi-C paired-end sequencing reads were mapped to the SNP-masked hg19 human genome using HiC-Pro software (version 2.6.0; Servant et al., 2015: PMID: 26619908) as follows. First, we obtained phased genotype VCF files for NA07000 and NA07056 cell lines from 1000 Genomes Project (version v5a.20130502), and generated two SNP-masked (i.e. alternative/reference and alternative/alternative SNP genotype loci were masked with N) hg19 genomes files for these two cell lines. The individual reads in each mapped paired-end read are evaluated for the presence of heterozygous SNPs and labeled as one of the following using phased genotype data from 1000 Genomes Project: parent-1 allele (M), parent-2 allele (P), or allele unassigned (UA). The M-M, M-UA and UA-M paired-end reads were grouped as ‘parent-1’ and P-P, P-UA and UA-P paired-end reads were grouped as ‘parent-2’ to compute chromatin interaction frequencies on two homologous chromosomes (G1 is SLE non-risk haplotype and G2 is SLE risk haplotype) at 5kb resolution for each replicate library. Raw interaction frequency count sparse matrices G1 (non-risk) and G2 (risk) were generated. The IDs of two 5kb regions from the first two columns in the matrix files are decoded in the dictionary file hg19_HiC_region_Ids_chr8.bed.
To identify differences in cis-interaction frequencies of homologous chromosomes 8 harboring risk and non-risk haplotypes, we determined haplotype-specific (G1 and G2) interaction frequency matrices in 5kb bins for each replicate library. For n replicate libraries from each cell line, we computed n matrices for G1 haplotype and n matrices for G2 haplotype. For NA07000, we used n = 5 (p1, p2, p3, p4 and p5). For NA07056, we used n = 4 (p1_a, p1_b, p2_a and p2_b). Treating the entries of these matrices as sequence count data with the study design (G1, G1, G1, G1, G1, G2, G2, G2, G2, G2) for NA07000 and the study design (G1, G1, G1, G1, G2, G2, G2, G2) for NA07056, we determined differential chromatin interactions using multiHiCcompare (version 1.10.0) method (Stansfield et al., 2019: PMID: 30668639) with the following parameters: make_hicexp(zero.p=0.8, A.min=5), cyclic_loess(span = 0.2), logfc_cutoff = 0.5, logcpm_cutoff = 0.5, p.method = ‘fdr’ and p.adj_cutoff = 0.05. The differential interactions are reported in the supplementary files *FDR5.csv. The interactions with positive log2FC (base-2 log fold-change) values are stronger on the risk haplotype than on the non-risk haplotype, and those with negative log2FC are weaker on the risk haplotype than on the non-risk haplotype.
Assembly: hg19
Supplementary files format and content: HiC-Pro output raw cis-interactions count matrices (*.matrix) in sparse 3-column format. Columns 1 and 2 contain IDs of pairs of 5kb regions on chromosome 8; third column contains the raw cis-interaction frequency of the two regions.
Supplementary files format and content: hg19_HiC_region_IDs_chr8.bed file contains IDs of 5kb regions on chromosome 8

Submission date

Aug 15, 2022

Last update date

Sep 07, 2022

Contact name

Iouri Chepelev

E-mail(s)

ichepelev@gmail.com

Organization name

US Department of Veterans Affairs Medical Center

Street address

3200 Vine St