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| Status |
Public on Sep 30, 2022 |
| Title |
5KO,DMSO,HiC,rep2 |
| Sample type |
SRA |
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| Source name |
#55
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| Organism |
Mus musculus |
| Characteristics |
cell line: #55
cell type: iMEFs
genotype: 5KO
treatment: DMSO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Hi-C experiments were performed based on DpnII enzyme (4-bps cutter) using 2×106 fixed cells. Hi-C libraries were subject to paired-end sequencing (150 base pair (bp) read length) using HiSeq X Ten. Detailed protocol for HiC-seq library preparation is available at Protocols.io (https://www.protocols.io/view/iconhi-c-protocol-ver-1-0-4mjgu4n).
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| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Hi-C data processing was done by using Docker for 4DN Hi-C pipeline (v43, https://github.com/4dn-dcic/docker-4dn-hic). The pipeline includes alignment (using the mouse genome, mm10) and filtering steps.
After filtering valid Hi-C alignments, .hic format Hi-C matrix files were generated by Juicer Tools
Assembly: mm10
Supplementary files format and content: hic
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| Submission date |
Sep 30, 2022 |
| Last update date |
Oct 01, 2022 |
| Contact name |
Kei Fukuda |
| E-mail(s) |
kefukuda8@gmail.com
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| Organization name |
RIKEN
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| Lab |
Cellular memory
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| Street address |
2-1 Hrosawa, Wakoshi
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| City |
Saitama |
| State/province |
Japan |
| ZIP/Postal code |
351-0198 |
| Country |
Japan |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE200012 |
Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway [Hi-C] |
| GSE200016 |
Spatial organization of H3K9me2/3-marked heterochromatin is redundantly maintained by either the H3K9 or H3K27 methylation pathway |
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| Relations |
| BioSample |
SAMN31111913 |
| SRA |
SRX17767693 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6612270_HiC_5KO-DMSO-rep2.ff.filter_same.MAPQ10.hic |
117.7 Mb |
(ftp)(http) |
HIC |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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