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| Status |
Public on Nov 03, 2023 |
| Title |
D200 HiC |
| Sample type |
SRA |
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| Source name |
Retinal organoid
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Retinal organoid
time: D200
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C was performed on 8-10 organoids from each time point according to the manufacturer’s instruction of Arima Genomics. In brief, organoids were dissociated to single cell following an optimized protocol of papain system (Fadl, et al., 2020) and then crosslinked with 2% paraformaldehyde (PFA, FDNeuroTechnologies) for 10 min. Subsequently, the crosslinked samples were quenched by 125 mM glycine for 5 min and frozen until use at -80 ℃ until use for Hi-C experiments. Freshly dissected human retina tissue was crosslinked with 1% formaldehyde in PBS for 10 min, quenched with 125 mM glycine for 5 min and frozen until use for Hi-C experiments. Before processing for Hi-C, samples were crosslinked again in 2% formaldehyde for 10 minutes, then quenched with 125 mM glycine 5 min. For HCT116 cell line (ATCC, VA, USA), 7x106 cells were crosslinked with 2% formaldehyde for 10 min, quenched for 5 min with stop solution I, lysed, and processed for Hi-C using ARIMA-Hi-C kit.
Hi-C was performed on isolated nuclei using Arima-Hi-C kit (Arima Genomics, CA, USA) and Hyper Prep DNA-seq library prep kit (KK8502; Kapa Biosciences, MA, USA), following the manufacturers’ instructions. The libraries were sequenced on HiSeq 2500 platform (Illumina, CA, USA) at a read length of 101 to 126 base pairs and approximately 600 million read pairs per sample.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Hi-C analysis was performed with HiCUP (Wingett et al., 2015) using Arima-specific in silico digested hg38 genome for the retina samples and the HCT116.
Filtered bam files produced by HiCUP have been converted to .hic files using Juicer (Durand et al., 2016) and to HOMER (Heinz et al., 2013; Heinz et al., 2018) tag directories.
mcool files were made using the hicConvertFormat tool from HiCExplorer.
Compartments have been called using HOMER using 100kb sliding windows with a step of 50kb (using options superRes and res, respectively)
Loops were called with Mustache
TADs calling has been performed on the merged samples using domaincaller (Dixon et al., 2012), using raw contact maps of 10kb bins.
TAD cliques were defined as described previously (Ali et al., 2021). Briefly, significant TAD-TAD interactions were found using the NCHG (Paulsen, et al., 2014) tool with the default settings then TAD cliques were identified via the igraph R package. 100 sets of random TAD cliques were generated by shuffling the size of cliques among the TADs.
We computed the total number of loop feet coverage using 30kb genomic windows with a step of 3kb using bedtools. For each sample, we selected the windows with a minimum coverage of 5 loop feet and stitched them together allowing a gap of up to 30kb between two windows using bedtools. We then merged these regions across samples and, for each sample, computed the total number of loop feet covering each region. For each sample, we selected the regions overlapping with at least 5 loop feet as a hub for further analysis.
We computed the organoids gene networks by integrating 5kb resolution loops and genes, associated to their expression level, at each time point. Genes overlapping and genes interacting through chromatin loops were associated into communities using home-made scripts
We computed the organoids loops networks using the method described previously (Phanstiel et al., 2017) using consensus, gained and lost loops at 5kb resolution.
We calculated domain score for each consensus TAD i.e., the ratio of intra-TAD contacts to inter-TAD contacts as defined previously (Krijger, et al., 2016)
Assembly: GRCh38.p7 and Ensembl v102
Supplementary files format and content: DXXX.hic - .hic formatted contact map
Supplementary files format and content: DXXX.compartments.PC1.bedGraph - bedGraph file showing the PC1 scores calculated by DomainCaller and used to identify compartment types
Supplementary files format and content: DXXX_TADs_10kb.bed - BED file identifying TADs as called by domaincaller
Supplementary files format and content: TAD_TAD_clique_size_DXXX.bed - BED file listing TAD locations and the number of significantly interacting TADs identified
Supplementary files format and content: DXXX.mcool - mcool formatted contact map
Supplementary files format and content: Domain_scores.tsv - Domain scores for each consensus TAD
Supplementary files format and content: loops_community_coord.bedpe - Bedpe file listing loop community participants by community and type of community
Supplementary files format and content: loops_hubs_with_loop_feet_counts.txt - TSV file showing the position of hubs and detailing the number of loops present in that hub at each time point
Supplementary files format and content: DXXX_loops_mustache.bedpe - Bedpe file showing loops called by mustache at this point
Supplementary files format and content: Loop_comparison_5kb_gaps.csv -CSV summarizing presence or absence of loops across samples
Supplementary files format and content: Loop_comparison_5kb_gaps_with_counts.csv -CSV summarizing presence or absence of loops across samples with contact counts for each loop
Supplementary files format and content: DXXX_genes_communities.txt - TSV file showing the members of each gene community
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| Submission date |
Apr 13, 2023 |
| Last update date |
Nov 03, 2023 |
| Contact name |
Zachary A Batz |
| Organization name |
NIH
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| Department |
NEI
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| Lab |
NNRL
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| Street address |
6 Center Dr Bldg 6, Rm 303
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE229681 |
Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids |
| GSE229683 |
Stage-specific dynamic reorganization of genome topology shapes transcriptional neighborhoods in developing human retinal organoids |
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| Relations |
| SRA |
SRX19962228 |
| BioSample |
SAMN34175124 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7173202_D200.compartments.PC1.bedGraph.gz |
830.7 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM7173202_D200.hic |
2.1 Gb |
(ftp)(http) |
HIC |
| GSM7173202_D200.mcool |
1.8 Gb |
(ftp)(http) |
MCOOL |
| GSM7173202_D200_TADs_10kb.bed.gz |
21.4 Kb |
(ftp)(http) |
BED |
| GSM7173202_TAD_TAD_clique_size_D200.bed.gz |
1.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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