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| Status |
Public on Sep 15, 2022 |
| Title |
CH12_HiC_shMcm_2 |
| Sample type |
SRA |
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| Source name |
CH12
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| Organism |
Mus musculus |
| Characteristics |
cell line: CH12
knockdown: shMcm
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| Growth protocol |
CH12 cells cultured in complete RPMI medium wit IL4/CD40/TGF beta stimulation.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA from crosslinked nuclei was digested with restriction enzyme, biotin filled ligated and streptavidin enriched
Libraries were prepared following standard Illumina protocols
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
CH12_HiC_shMcm.mcool
CH12_HiC_shMcm_5kb_domains.bed
CH12_HiC_shMcm_20kb_w200000.PC1.bw
CH12_HiC_shMcm_hiccups.bed
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| Data processing |
Hi-C
Raw paired-end reads were controlled for quality and adapters were removed with trim_galore 0.6.2 with a quality cutoff of 20
Trimmed read pairs were processed with HICUP 0.7.3 using ^GATC,MboI as restriction enzyme and mouse mm9 as reference genome
Aligned, filtered and deduplicated read pairs were converted to pairix with cooler csort 0.8.3
Resulting pairix files were then used to generate a 5kb initial contact matrix using cooler cload pairix 0.8.3 with canonical chromosome sizes of mm9 and cooler zoomify 0.8.3 was used to generate resolutions of 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb
Each resolution was then balanced using genome-wide KR (0.05, part of HiCExplorer) and IC (part of cooler 0.8.3) using default arguments and saved into a multicooler file
Similarly, juicer_tools 1.22.01 was used to generate hic files of the same resolutions and balanced with GW_KR for subsequent loop calling
Loops were then called with HICCUPS 1.22.01 with arguments -m 1024 -r 5000,10000,25000 -f 0.1,0.1,0.1 -k GW_KR -p 4,2,1 -i 7,5,3 -t 0.02,1.5,1.75,2 -d 20000,20000,50000
In addition, HOMER 4.10 was used to compute compartment signals and TAD annotations by first generating a ditag directory from HICUP results using makeTagDirectory. Subsequently, compartment signals were computed with runHiCpca.pl with -res 20000 -window 200000 -genome mm9 using the RefSeq gene annotation for mm9 as markers of the active compartment. TADs were called with findTADsAndLoops.pl find with -res 5000 -balance -window 50000 -genome mm9 using known duplications for mm9 (downloaded from UCSC) as bad regions.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: Multicoolers contain the raw contact matrixes as well as balancing weights for KR and IC algorithms for resolutions of 5kb, 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb. Balancing weights for each resolution were saved in the bins table as 'weight' (KR) and 'ICE' (IC) column, respectively
Supplementary_files_format_and_content: Loop annotions were converted from the HICCUPs merged_loops.bedpe file to a 2D bed file containing columns chr1, x1, x2, chr2, y1, y2, fdrBL
Supplementary_files_format_and_content: TAD annotations were converted from to a domains file with columns chr, start, end, name, TADscore, strand, start, end, RGB color
Supplementary_files_format_and_content: The first principal component as computed by homer was converted to bigWig with sort -k1,1 -k2,2n; bedGraphToBigWig (UCSC kent_tools/20190507-linux.x86_64) with a chromsize file containing only mm9 canonical chromosomes
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| Submission date |
Nov 19, 2020 |
| Last update date |
Sep 15, 2022 |
| Contact name |
Tobias Neumann |
| Organization name |
IMP
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| Street address |
Campus-Vienna-Biocenter 1
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| City |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE161817 |
DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations [HiC] |
| GSE161822 |
DNA replication timing directly regulates the frequency of oncogenic chromosomal translocations |
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| Relations |
| BioSample |
SAMN16837305 |
| SRA |
SRX9532347 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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