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| Status |
Public on Feb 13, 2019 |
| Title |
Hi-C library corrected 2 rep 1 |
| Sample type |
SRA |
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| Source name |
Hi-C library corrected 2
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| Organism |
Homo sapiens |
| Characteristics |
cell type: human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM)
cell line: R225R LMNA corrected 2 hiPSCs
time point: Day 14 of cardiac differentiation
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| Treatment protocol |
Cells were fixed using 2% formaldehyde for 10 minutes.
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| Growth protocol |
Human induced pluripotent stem cells (hiPSCs) were cultured and differentiated into cardiomyocytes (hiPSC-CM) with minor modifications of previously described methods (Burridge et al., 2014; Fields et al., 2017). hiPSCs were cultured on plates pre-coated with 0.5 µg/cm2 recombinant human Laminin-521 matrix (rhLaminin521; Biolamina) with daily changes of antibiotic-free Essential 8 (E8) media (ThermoFisher). Cells were passaged as small clumps with Versene (ThermoFisher), and 10 µM Y-27632 (Tocris) was added for the first 16 hr. For hiPSC-CM generation, cells were passaged as single cells with Versene, and seeded at a density of 2.5 x 105 per well of a 12-well plate pre-coated with 2 µg/cm2 rhLaminin521 (denoted day -2). After 24 hr media was changed to E8 with 1 µM CHIR-99021 (Cayman), denoted day -1. On day 0 media was changed to RBA media (RPMI 1640 with glutamine, ThermoFisher, supplemented with 500 µg/ml BSA and 213 µg/ml ascorbic acid, both from Sigma-Aldrich) supplemented with 4 µM CHIR-99021. At day 2, media was changed to RBA with 2 µM WNT-C59 (Selleckchem). On day 4, media was changed to RBA. On day 6, media was changed to RPMI-B27 media (RPMI with 1x B-27 supplement, both from Thermo Fisher), with further media changes every other day. Beating was first observed between day 7 and day 9, and cells were cultured until day 14 before collection.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed using 10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 0.2% Igepal CA-630, 1x Protease Inhibitor in ddH2O
Library prep was carried out using the in situ DNase Hi-C protocols (V. Ramani et al. Nat Protoc. 2016). Samples were barcoded during final library PCR and samples were demultiplexed prior to downstream analysis. Each library was sequenced two independent times, and the results were merged during downstream analysis.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Reads were mapped with BWA-MEM version 0.7.13 to hg38 using default parameters. Secondary mappings were filtered out with samtools.
Primary mappings were processed using HIC-PRO version 2.7.6, excluding pairs less than 1KB apart and excluding MAPQ scores <30, to generate validPairs files and ICED normalized counts, outputed as a bed file of bins and a three column file of bins and contact counts.
validPair files were used as input for HOMER version 4.7 at 500KB resolution to generate PC1 values (A/B compartment calls).
Genome_build: hg38
Supplementary_files_format_and_content: allValidPairs file is processed output from HiC-Pro and contains read name and mapping location for the two reads after passing distance and quality threshold
Supplementary_files_format_and_content: iced.matrix file is the 3 column counts matrix (Bin1, Bin2, counts) corresponding to the bins.bed file at 500KB resolution, output from HiC-Pro.
Supplementary_files_format_and_content: PC1.bedGraph files are the ouput from HOMER on the processed Hi-C data, representing the A/B compartment calls, in bedGraph format (coordinates and score)
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| Submission date |
Feb 12, 2019 |
| Last update date |
Feb 13, 2019 |
| Contact name |
Alessandro Bertero |
| E-mail(s) |
abertero@uw.edu
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| Organization name |
University of Washington
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| Department |
Institute for Stem Cell and Regenerative Medicine
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| Street address |
850 Republican St
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (2) |
| GSE126459 |
Gene expression and chromatin organization changes in lamin A/C haploinsufficient human induced pluripotent stem cell-derived cardiomyocytes [Hi-C] |
| GSE126460 |
Gene expression and chromatin organization changes in lamin A/C haploinsufficient human induced pluripotent stem cell-derived cardiomyocytes |
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| Relations |
| BioSample |
SAMN10921583 |
| SRA |
SRX5369389 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3602090_HiC_corrected.2_rep1_500000_iced.matrix.gz |
87.4 Mb |
(ftp)(http) |
MATRIX |
| GSM3602090_HiC_corrected.2_rep1_500KB_Active.PC1.bedGraph.gz |
72.0 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM3602090_HiC_corrected.2_rep1_allValidPairs.pairs.txt.gz |
987.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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