|
| Status |
Public on Oct 02, 2019 |
| Title |
GM19141 Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Lymphoblastoid Cell Lines
|
| Organism |
Homo sapiens |
| Characteristics |
restriction enzyme: HindIII
cell line: GM19141
|
| Biomaterial provider |
https://www.coriell.org/0/Sections/Search/Sample_Detail.aspx?Ref=GM19141
|
| Growth protocol |
Lymphoblastoid lines were grown according to guidelines from Coriell: https://www.coriell.org/0/PDF/Lymphoblast_Culture_FAQ.pdf. Cells for Hi-C replicates were grown independently for at least 2 passages.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were crosslinked in 1% formaldehyde for 10 min, quenched with 2.5M Glycine for 5 min, collected by centrifugation, and snap frozen in liquid nitrogen. These cell pellets were used as input for Hi-C library construction.
HindIII Hi-C performed as previously reported in Lieberman-Aiden et al., 2009. (PMID: 19815776)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
HiSeq 2000 and HiSeq 2500
|
| Data processing |
Library strategy: Hi-C
Read ends were aligned to the hg19 reference genome using BWA MEM 0.7.8-r455 as single-end reads using a modified WASP pipeline (PMID: 26366987) to control for potential allelic mapping biases. Briefly, aligned reads were further processed to keep only the five prime alignment, and reads with low mapping quality (<10) were filtered out. Read ends were then paired together manually. PCR duplicates were removed using Picard tool.
Intra-chromosomal read pairs that are at least 20Kb away were further divided into 40Kb bin pairs based on five prime positions. Number of read pairs in each 40Kb bin pairs were aggregated to the contact matrices per chromosome. Raw counts in the contact matrices were then normalized using HiCNorm (PMID: 23023982) to remove potential biases.
Normalized matrices were further quantile normalized across replicates and samples to remove possible batch effects.
PC1 scores were computed using methods defined previously (Lieberman-Aiden et al., 2009; PMID: 19815776).
Directional Index (DI) was computed as previously described (Dixon et al. 2012; PMID: 22495300).
Insulation scores were computed by adapting previous methods (Crane et al., 2015; PMID: 26030525).
FIRE scores were computed using HiCNormCis as described in Schmitt et al. 2016. (PMID: 27851967)
Phasing of variants was performed based on Haploseq pipeline. (PMID: 24185094 )
Genome_build: hg19
Supplementary_files_format_and_content: Contact matrices are NxN matrices in compressed text format. PC1, DI, IS, and FIRE scores are in bigwig format. Phased SNPs are in VCF format.
|
| |
|
| Submission date |
Mar 21, 2019 |
| Last update date |
Dec 06, 2019 |
| Contact name |
Yunjiang Qiu |
| Organization name |
University of California, San Diego
|
| Street address |
9500 Gilman Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE128678 |
Common DNA sequence variation influences 3-dimensional conformation of the human genome |
|
| Relations |
| BioSample |
SAMN11231348 |
| SRA |
SRX5558241 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3682179_GM19141_Rep2.40Kb.2Mb.HiCNorm_quantile.DI.bw |
808.5 Kb |
(ftp)(http) |
BW |
| GSM3682179_GM19141_Rep2.40Kb.400Kb.HiCNorm_quantile.IS.bw |
833.2 Kb |
(ftp)(http) |
BW |
| GSM3682179_GM19141_Rep2.40Kb.HiCNormCis_quantile.FIRE.bw |
773.6 Kb |
(ftp)(http) |
BW |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr1.mat.gz |
16.8 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr10.mat.gz |
8.2 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr11.mat.gz |
7.9 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr12.mat.gz |
7.8 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr13.mat.gz |
5.9 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr14.mat.gz |
4.6 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr15.mat.gz |
3.7 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr16.mat.gz |
3.1 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr17.mat.gz |
2.9 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr18.mat.gz |
4.1 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr19.mat.gz |
1.4 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr2.mat.gz |
19.8 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr20.mat.gz |
2.4 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr21.mat.gz |
1.1 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr22.mat.gz |
888.8 Kb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr3.mat.gz |
15.4 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr4.mat.gz |
14.6 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr5.mat.gz |
13.0 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr6.mat.gz |
12.3 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr7.mat.gz |
10.3 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr8.mat.gz |
9.8 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chr9.mat.gz |
6.1 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.chrX.mat.gz |
7.4 Mb |
(ftp)(http) |
MAT |
| GSM3682179_GM19141_Rep2.40Kb.HiCNorm_quantile.pc1.bw |
654.3 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
