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| Status |
Public on Jun 13, 2023 |
| Title |
CH12_HiC_Rif1KO_shLacZ |
| Sample type |
SRA |
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| Source name |
CH12
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| Organism |
Mus musculus |
| Characteristics |
cell type: CH12 Rif1KO cells
treatment: shLacZ
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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 |
HiC
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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
In addition, HOMER 4.10 was used to compute compartment signals 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.
Assembly: 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: hic files contain the raw contact matrixes as well as balancing weights for GW_KR resolutions of 5kb, 10kb, 20kb, 25kb, 50kb, 100kb, 200kb, 250kb, 500kb, 1Mb
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 |
Apr 03, 2023 |
| Last update date |
Jun 13, 2023 |
| 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) |
| GSE228876 |
RIF1 regulates replication origin activity and early replication timing in B cells [HI-C] |
| GSE228880 |
RIF1 regulates early replication timing in murine B cells. |
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| Relations |
| BioSample |
SAMN34060503 |
| SRA |
SRX19857848 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7140986_CH12_HiC_Rif1KO_shLacZ.hic |
1.4 Gb |
(ftp)(http) |
HIC |
| GSM7140986_CH12_HiC_Rif1KO_shLacZ.mcool |
1.1 Gb |
(ftp)(http) |
MCOOL |
| GSM7140986_CH12_HiC_Rif1KO_shLacZ_20kb_PC1.bedGraph.gz |
1.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM7140986_CH12_HiC_Rif1KO_shLacZ_20kb_PC1.bw |
1.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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