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| Status |
Public on Mar 23, 2021 |
| Title |
WT rep1 |
| Sample type |
SRA |
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| Source name |
whole worms
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| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2
developmental stage: mixed embryo
genotype: Wild-type
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| Treatment protocol |
Embryos were treated with 2% formaldehyde for 30 minutes, washed with M9, and collected by centifugation and freezing at -80C until extract preparation.
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| Growth protocol |
Embryos were isolated by bleaching gravid adults grown on plates at 20C.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen embryos were then resuspended in and crosslinked with 2% formaldehyde in M9 for another 30 mins. The embryos were spun down at 6000g for 30 sec and washed once with 100mM Tris Cl pH 7.5 and twice with M9. The embryo pellet was resuspended in 1 ml embryo buffer (110 mM NaCl, 40 mM KCl, 2 mM CaCl2, 2 mM MgCl2, 25 mM HEPES-KOH pH 7.5) containing 1 unit chitinase (Sigma), digested approximately 15 minutes, blastomeres were washed with embryo buffer twice by spinning at 1000g 5 min. The pellet was resuspended in Nuclei Buffer A (15 mM Tris HCl pH 7.5, 2 mM MgCl2,0.34 M Sucrose,0.15 mM Spermine, 0.5 mM Spermidine, 1 mM DTT,0.5 mM PMSF (1X Calbiochem Protease Inhibitor cocktail I), 0.25% NP-40, 0.1% Triton X-100), centrifuged at 1000g for 5 minutes at 4C then resuspended in 1.5 mL Nuclei Buffer A. The embryos were then dounced 10X with a loose pestle and 10X with a tight pestle. The nuclei were separated from the cellular debris through spinning down the dounced material at 200G, then collecting the supernatant containing the nuclei into a separate tube. The pellet was resuspended in 1.5mL and the douncing process was repeated four times. Each individual supernatant containing nuclei was checked for quality by DAPI staining and those without debris were pooled and spun down at 1000G for 10 mins at 4C. Approximately 20 ul nuclei pellet were used to proceed to Arima Hi-C per the manufacturer's instructions.
Library preparation was performed using the KAPA Hyper Prep Kit using the protocol provided by Arima.
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ExpFLIP_insulation_N2_DJ73_DJ74_10000_score.bedgraph
ExpBLOCK_DJ73_10000_score.bedgraph
ExpTRIPLE_insulation_N2_DJ73_DJ74_2000_score.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_center.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_left.bedgraph
ExpTRIPLE_4C_DJ73_DJ74_2000_sw3_right.bedgraph
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| Data processing |
Basecalls were performed using CASAVA version 1.8.
Paired end Illumina sequence reads were mapped using default parameters of the juicer pipeline (version=1.5.7) as described in (Durand et al., 2016). For insertions and fusion strains, the reference genome was modified to match the genetic changes. For downstream analysis, inter_30.hic outputs from juicer pipeline were converted to h5 file to be used in HiCExplorer (version=3.5.1)(Ramirez et al., 2018; Wolff et al., 2018). Matrices of replicates were combined using hicSumMatrices. Each replicate or each summed matrix were normalized to match the depth of the smallest matrix in comparison using hicNormalize with the option --smallest. The replicate and summed matrices were ICE normalized using hicCorrectMatrix with the following parameters: --correction_method ICE, -t 1.7 5, --skipDiagonal, --chromosomes I II III IV V X or I II III IV XV for X-V fusion.
The insulation scores were computed using the 10kb-binned normalized matrix function hicFindTADs with the following parameters: --correctForMultipleTesting fdr, --minDepth 80000, --maxDepth 200000, --step 40000. For 2kb-binned normalized matrix, the following parameters were used: --correctForMultipleTesting fdr, --minDepth 16000, --maxDepth 40000, --step 8000. Output score.bedgraph was compared between experimental conditions. The bedgraph file was converted to bigwig using BedgraphToBigwig utility provided from UCSC website (Kent, Zweig, Barber, Hinrichs, & Karolchik, 2010).
In silico 4C plots were generated using the chicViewpoint function of hicexplorer with the following parameters: --averageContactBin 3 --range 20000000 20000000. The plotted values indicate relative contact scores out of 1000. The background model for chicViewpoint was generated using the summed wildtype matrix using the chicViewpointBackgroundModel function.
Genome_build: WS220
Supplementary_files_format_and_content: hic matrix files
Supplementary_files_format_and_content: bedgraphs containing insulation scores
Supplementary_files_format_and_content: bedgraphs containing in silico 4C
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| Submission date |
Mar 23, 2021 |
| Last update date |
Jun 23, 2022 |
| Contact name |
Jun Kim |
| E-mail(s) |
kimj50@nyu.edu
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| Phone |
7183094777
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| Organization name |
NYU
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| Department |
Biology
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| Lab |
Ercan
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| Street address |
100 Washington Square East 1009 Silver Center
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| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10003 |
| Country |
USA |
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| Platform ID |
GPL26672 |
| Series (2) |
| GSE168803 |
Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans |
| GSE169468 |
Condensin DC spreads linearly and bidirectionally from recruitment sites to create loop-anchored TADs in C. elegans (Hi-C) |
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| Relations |
| BioSample |
SAMN18445200 |
| SRA |
SRX10425218 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5206715_DJ73_inter_30.hic |
739.3 Mb |
(ftp)(http) |
HIC |
| GSM5206715_ExpBLOCK_DJ73_10000_score.bedgraph.gz |
112.3 Kb |
(ftp)(http) |
BEDGRAPH |
| GSM5206715_ExpXV_DJ73_ypT47_10000_score.bedgraph.gz |
85.2 Kb |
(ftp)(http) |
BEDGRAPH |
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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