Welcome to ChromOS

NGS Samples

Tissues (Cells)

Registered Users

Example: [OLP-1-608]
HiC collection
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Introduction

ChromOS services online access to the data resources from Chromosome Orchestration System (OS) , a research project supported by MEXT Japan.

Chromosomes play a fundamental role in many biological processes. Previous research efforts have advanced our understanding of specific chromosomal events, such as DNA transcription, replication, recombination, partitioning, and epigenetic modification. One of the major future challenges in chromosome biology will be to provide an overall framework of how these individual activities are orchestrated and coordinated to maximize their effects in a variety of biological processes that evolve over time. The main goal of this project is to describe the mechanisms that regulate the functional unity of the chromosomes (chromosome OS) by thoroughly examining the structural relationship between, and the hierarchy of, individual chromosomal functions.

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Recently Submitted Data

Accession	Cell	Organism	Restriction enzyme	Condition	Run ID
OLP-2-620	RPE	human	MboI	ESCO1, 2 KD (siRNA transfection 48 h), No Sync	1809JNHX-0004_si11-19_res
OLP-2-614	RPE	human	MboI	RAD21 KD (siRNA transfection 72 h), No Sync	1809JNHX-0003_si621_res
OLP-2-628	RPE	human	MboI	PDS5B KD (siRNA transfection 48 h), No Sync	HN00102383_si91_res
OLP-2-621	RPE	human	MboI	MAU2 KD (siRNA transfection 72 h), No Sync	1809JNHX-0004_si251_res
OLP-2-613	RPE	human	MboI	RAD21 KD (siRNA transfection 72 h), No Sync	1809JNHX-0003_si7-621_res
OLP-2-623	RPE	human	MboI	CTCF KD (siRNA transfection 72 h), No Sync	1811KHX-0110_R_626_628_d3_res
OLP-2-624	RPE	human	MboI	WAPL KD (siRNA transfection 48 h), No Sync	HN00102380_si31_res
OLP-2-625	RPE	human	MboI	PDS5A KD (siRNA transfection 72 h), No Sync	HN00102380_si88_d3_res
OLP-2-619	RPE	human	MboI	ESCO1 KD (siRNA transfection 48 h), No Sync	1809JNHX-0004_si11_res
OLP-2-626	RPE	human	MboI	JQ1 (BRD Inhibitor), No Sync	HN00102383_JQ1_plus_res
OLP-2-615	RPE	human	MboI	Control, No Sync	1807JNHX-0018_Ctrl_res
OLP-2-627	RPE	human	MboI	PDS5A,B KD (siRNA transfection 48 h), No Sync	HN00102383_si88_91_res
OLP-2-616	RPE	human	MboI	Control, No Sync	1809JNHX-0003_Ctrl_res
OLP-2-618	RPE	human	MboI	CTCF KD (siRNA transfection 72 h), No Sync	1811KHX-0109_FT_WT_res
OLP-2-617	RPE	human	MboI	CTCF KD (siRNA transfection 72 h), No Sync	1809JNHX-0003_si628_res
OLP-2-622	RPE	human	MboI	Control, No Sync	1811KHX-0109_R_Ctrl_res
OLP-2-629	LCL	human	MboI	WT, No Sync	1904JNHX-0009_GIA_res
OLP-2-630	LCL	human	MboI	HP1beta mutation, No Sync	1904JNHX-0009_RIM_res
OLP-2-631	HCT116/Rad21-mAD/TIR1	human	MboI	NIPBL, exon3 frame-shift, No Sync	1903JNHX-0034_B3_res
OLP-2-633	HCT116/ESCO1-mAD/TIR1	human	MboI	Dox 12 h -> IAA 3 h (ESCO1 depletion), No Sync	1907JNHX-0026_E1_dox_iaa_res
OLP-2-632	HCT116/ESCO1-mAD/TIR1	human	MboI	Dox 16 h -> (control), No Sync	1908JNHX-0025_E1_dox_res
OLP-2-634	HCT116	human	MboI	NIPBL, exon 3 single allele mutation, No sync	1807JNHX-0018_HCT_3-3_res
OLP-2-635	HCT116	human	MboI	Wild Type, No Sync	1807JNHX-0018_HCT_Wt_res
OLP-2-641	fibroblast	human	MboI	WT, female, No Sync	1807JNHX-0018_GM2036_res
OLP-2-640	fibroblast	human	MboI	WT, female, No Sync	1904JNHX-0009_2036_res
OLP-2-639	fibroblast	human	MboI	CdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync	1807JNHX-0018_CdLS304_res
OLP-2-636	fibroblast	human	MboI	CdLS, NIPBL: 1372C>T;Q458X / Nonsense, female, No Sync	1807JNHX-0018_CdLS510_res
OLP-2-642	fibroblast	human	MboI	WT, male, No Sync	1807JNHX-0018_GM3348_res
OLP-2-638	fibroblast	human	MboI	CdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync	1807JNHX-0018_CdLS087_res
OLP-2-637	fibroblast	human	MboI	WT, male, No Sync	1807JNHX-0018_CdLS006_res
OLP-2-643	Blood Cell Stem Cell	mouse	MboI	STAG2 conditional KO	1811KHX-0110_KO_561_res
OLP-2-646	Blood Cell Stem Cell	mouse	MboI	STAG2 conditional KO	1811KHX-0110_KO_544_res
OLP-2-645	Blood Cell Stem Cell	mouse	MboI	WT	1811KHX-0110_WT_546_res
OLP-2-644	Blood Cell Stem Cell	mouse	MboI	WT	1811KHX-0110_WT_563_res
OLP-2-654	293FT	human	MboI	WT, No Sync	1905JNHX-0006_FT_res
OLP-2-648	293FT	human	MboI	lentiviral vector Infection, Control, No Sync	1903JNHX-0034_FT-vi24_res
OLP-2-649	293FT	human	MboI	lentiviral vector Infection, Control, No Sync	1903JNHX-0035_FT-Wt_res
OLP-2-651	293FT	human	MboI	lentiviral vector Infection, Control, No Sync	1908JNHX-0026_vi24_res
OLP-2-652	293FT	human	MboI	Wild AFF4 lentiviral vector Infection, No Sync	1908JNHX-0026_vi27_res
OLP-2-647	293FT	human	MboI	Mutant AFF4 lentiviral vector Infection, No Sync	1903JNHX-0035_FT-vi28_res
OLP-2-653	293FT	human	MboI	Mutant AFF4 lentiviral vector Infection, No Sync	1908JNHX-0026_vi28_res
OLP-2-650	293FT	human	MboI	NIPBL, exon 3 bi-allele mutation, No Sync	1811KHX-0109_FT_ND1_res

How to Use

ChromOS manages the data from the project "Chromosome OS".
ChromOS provides the analytic pipeline for Hi-C data by collaborating with OpenLooper (OLP).
Registration via OpenLooper is required. Thereby, users can manage the data and submit jobs to analyze. Learn more..
Anyone can freely access the data opened by the registered users.

How to Run Hi-C pipeline

To reduce BAM filesize, prepare one chromosome per BAM.
"Samtools view" command will be helpful to do it.

Data Sharing (OpenLooper)

OpenLooper (OLP) collects genome-wide data on chromatin structures investigated by various high-throughput experimental assays. Simultaneously, OLP provides a platform that supports opening and sharing the data.

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Genome Browser

A web-based genome browser displays multiple processed NGS data in interactive multi-tracks. The users can access it directly or through the data browser that provides selectable individual assay .

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Hi-C Analysis

ChromOS runs a pipeline for Hi-C data analysis with user-uploaded BAM files via OpenLooper. This pipeline is now in service (2020.06).

Example: [OLP-1-608]
HiC collection: [RPE, HCT116, LCL,...]