Welcome to ChromOS

NGS Samples

Tissues (Cells)

Registered Users

Example: [OLP-1-608] 
HiC collection 
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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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Accession Cell Organism Restriction enzyme Condition Run ID
OLP-2-620 RPEhumanMboIESCO1, 2 KD (siRNA transfection 48 h), No Sync1809JNHX-0004_si11-19_res
OLP-2-614 RPEhumanMboIRAD21 KD (siRNA transfection 72 h), No Sync1809JNHX-0003_si621_res
OLP-2-628 RPEhumanMboIPDS5B KD (siRNA transfection 48 h), No SyncHN00102383_si91_res
OLP-2-621 RPEhumanMboIMAU2 KD (siRNA transfection 72 h), No Sync1809JNHX-0004_si251_res
OLP-2-613 RPEhumanMboIRAD21 KD (siRNA transfection 72 h), No Sync1809JNHX-0003_si7-621_res
OLP-2-623 RPEhumanMboICTCF KD (siRNA transfection 72 h), No Sync1811KHX-0110_R_626_628_d3_res
OLP-2-624 RPEhumanMboIWAPL KD (siRNA transfection 48 h), No SyncHN00102380_si31_res
OLP-2-625 RPEhumanMboIPDS5A KD (siRNA transfection 72 h), No SyncHN00102380_si88_d3_res
OLP-2-619 RPEhumanMboIESCO1 KD (siRNA transfection 48 h), No Sync1809JNHX-0004_si11_res
OLP-2-626 RPEhumanMboIJQ1 (BRD Inhibitor), No SyncHN00102383_JQ1_plus_res
OLP-2-615 RPEhumanMboIControl, No Sync1807JNHX-0018_Ctrl_res
OLP-2-627 RPEhumanMboIPDS5A,B KD (siRNA transfection 48 h), No SyncHN00102383_si88_91_res
OLP-2-616 RPEhumanMboIControl, No Sync1809JNHX-0003_Ctrl_res
OLP-2-618 RPEhumanMboICTCF KD (siRNA transfection 72 h), No Sync1811KHX-0109_FT_WT_res
OLP-2-617 RPEhumanMboICTCF KD (siRNA transfection 72 h), No Sync1809JNHX-0003_si628_res
OLP-2-622 RPEhumanMboIControl, No Sync1811KHX-0109_R_Ctrl_res
OLP-2-629 LCLhumanMboIWT, No Sync1904JNHX-0009_GIA_res
OLP-2-630 LCLhumanMboIHP1beta mutation, No Sync1904JNHX-0009_RIM_res
OLP-2-631 HCT116/Rad21-mAD/TIR1humanMboINIPBL, exon3 frame-shift, No Sync1903JNHX-0034_B3_res
OLP-2-633 HCT116/ESCO1-mAD/TIR1humanMboIDox 12 h -> IAA 3 h (ESCO1 depletion), No Sync1907JNHX-0026_E1_dox_iaa_res
OLP-2-632 HCT116/ESCO1-mAD/TIR1humanMboIDox 16 h -> (control), No Sync1908JNHX-0025_E1_dox_res
OLP-2-634 HCT116humanMboINIPBL, exon 3 single allele mutation, No sync1807JNHX-0018_HCT_3-3_res
OLP-2-635 HCT116humanMboIWild Type, No Sync1807JNHX-0018_HCT_Wt_res
OLP-2-641 fibroblasthumanMboIWT, female, No Sync1807JNHX-0018_GM2036_res
OLP-2-640 fibroblasthumanMboIWT, female, No Sync1904JNHX-0009_2036_res
OLP-2-639 fibroblasthumanMboICdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync1807JNHX-0018_CdLS304_res
OLP-2-636 fibroblasthumanMboICdLS, NIPBL: 1372C>T;Q458X / Nonsense, female, No Sync1807JNHX-0018_CdLS510_res
OLP-2-642 fibroblasthumanMboIWT, male, No Sync1807JNHX-0018_GM3348_res
OLP-2-638 fibroblasthumanMboICdLS, NIPBL:2479_2480delAG; R827GfsX2, No Sync1807JNHX-0018_CdLS087_res
OLP-2-637 fibroblasthumanMboIWT, male, No Sync1807JNHX-0018_CdLS006_res
OLP-2-643 Blood Cell Stem CellmouseMboISTAG2 conditional KO1811KHX-0110_KO_561_res
OLP-2-646 Blood Cell Stem CellmouseMboISTAG2 conditional KO1811KHX-0110_KO_544_res
OLP-2-645 Blood Cell Stem CellmouseMboIWT1811KHX-0110_WT_546_res
OLP-2-644 Blood Cell Stem CellmouseMboIWT1811KHX-0110_WT_563_res
OLP-2-654 293FThumanMboIWT, No Sync1905JNHX-0006_FT_res
OLP-2-648 293FThumanMboIlentiviral vector Infection, Control, No Sync1903JNHX-0034_FT-vi24_res
OLP-2-649 293FThumanMboIlentiviral vector Infection, Control, No Sync1903JNHX-0035_FT-Wt_res
OLP-2-651 293FThumanMboIlentiviral vector Infection, Control, No Sync1908JNHX-0026_vi24_res
OLP-2-652 293FThumanMboIWild AFF4 lentiviral vector Infection, No Sync1908JNHX-0026_vi27_res
OLP-2-647 293FThumanMboIMutant AFF4 lentiviral vector Infection, No Sync1903JNHX-0035_FT-vi28_res
OLP-2-653 293FThumanMboIMutant AFF4 lentiviral vector Infection, No Sync1908JNHX-0026_vi28_res
OLP-2-650 293FThumanMboINIPBL, exon 3 bi-allele mutation, No Sync1811KHX-0109_FT_ND1_res
  1. ChromOS manages the data from the project "Chromosome OS".
  2. ChromOS provides the analytic pipeline for Hi-C data by collaborating with OpenLooper (OLP).
  3. Registration via OpenLooper is required. Thereby, users can manage the data and submit jobs to analyze. Learn more..
  4. Anyone can freely access the data opened by the registered users.
Run_Hi-C
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.

Get started »

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 .

Get started »

Hi-C

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,...]


 In Focus Articles (last modified: 2021-01-22 08:23:52)

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.


Contessoto VG, Cheng RR, Hajitaheri A, Dodero-Rojas E, Mello MF, Lieberman-Aiden E, Wolynes PG, Di Pierro M, Onuchic JN (Nucleic Acids Res. 2021 01 08;49(D1):D172-D182)
We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence insitu hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic......
PubMed:33021634

The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis.


Hong P, Jiang H, Xu W, Lin D, Xu Q, Cao G, Li G (Genes (Basel). 2020 03 10;11(3):)
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (3D) genome organizations and gene regulation. Digestion-ligation-only Hi-C (DLO Hi-C) is a new technology with high efficiency and cost-effectiveness for whole-genome chromosome conformation capture. Here, we introduce the DLO Hi-C tool, a flexible and versatile pipeline for processing DLO Hi-C data from raw sequencing reads to normalized contact maps and for providing quality controls for different steps. It includes more efficient iterative mapping and linker filtering. We applied the DLO Hi-C tool to different DLO Hi-C datasets and demonstrated its ability in processing large data with multithreading. The DLO Hi-C tool is suitable for processing DLO Hi-C and in situ DLO Hi-C datasets. It is convenient and efficient for DLO Hi-C data processing....
PubMed:32164155

Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles.


Tao H, Li H, Xu K, Hong H, Jiang S, Du G, Wang J, Sun Y, Huang X, Ding Y, Li F, Zheng X, Chen H, Bo X (Brief Bioinform. 2021 Jan 18;:)
The exploration of three-dimensional chromatin interaction and organization provides insight into mechanisms underlying gene regulation, cell differentiation and disease development. Advances in chromosome conformation capture technologies, such as high-throughput chromosome conformation capture (Hi-C) and chromatin interaction analysis by paired-end tag (ChIA-PET), have enabled the exploration of chromatin interaction and organization. However, high-resolution Hi-C and ChIA-PET data are only available for a limited number of cell lines, and their acquisition is costly, time consuming, laborious and affected by theoretical limitations. Increasing evidence shows that DNA sequence and epigenomic features are informative predictors of regulatory interaction and chromatin architecture. Based on these features, numerous computational methods have been developed for the prediction of chromatin interaction and organization, whereas they are not extensively applied in biomedical study. A systematical study to summarize and evaluate such methods is still needed to facilitate their application. Here, we summarize 48 computational methods for the prediction of chromatin interaction and organi......
PubMed:33454752

A chromosome-level genome assembly provides new insights into paternal genome elimination in the cotton mealybug Phenacoccus solenopsis.


Li M, Tong H, Wang S, Ye W, Li Z, Omar MAA, Ao Y, Ding S, Li Z, Wang Y, Yin C, Zhao X, He K, Liu F, Chen X, Mei Y, Walters JR, Jiang M, Li F (Mol Ecol Resour. 2020 Nov;20(6):1733-1747)
Mealybugs (Hemiptera: Pseudococcidae) are economically important agricultural pests with several compelling biological phenomena including paternal genome elimination (PGE). However, limited high-quality genome assemblies of mealybugs hinder a full understanding of this striking and unusual biological phenomenon. Here, we generated a chromosome-level genome assembly of cotton mealybug, Phenacoccus solenopsis, by combining Illumina short reads, PacBio long reads and Hi-C scaffolding. The assembled genome was 292.54 Mb with a contig N50 of 489.8 kb and a scaffold N50 of 49.0 Mb. Hi-C scaffolding assigned 84.42% of the bases to five chromosomes. A total of 110.75 Mb (37.9%) repeat sequences and 11,880 protein-coding genes were predicted. The completeness of the genome assembly was estimated to be 95.5% based on BUSCO genes. In addition, 27,086 (95.3%) full-length PacBio transcripts were uniquely mapped to the assembled scaffolds, suggesting the high quality of the genome assembly. We showed that cotton mealybugs lack differentiated sex chromosomes by analysing genome resequencing data of males and females. DAPI staining confirmed that one chromosome set in males becomes heterochro......
PubMed:33460249

SPIN reveals genome-wide landscape of nuclear compartmentalization.


Wang Y, Zhang Y, Zhang R, van Schaik T, Zhang L, Sasaki T, Peric-Hupkes D, Chen Y, Gilbert DM, van Steensel B, Belmont AS, Ma J (Genome Biol. 2021 Jan 14;22(1):36)
We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for modulating genome function. As a proof-of-principle, we use SPIN to integrate nuclear compartment mapping (TSA-seq and DamID) and chromatin interaction data (Hi-C) from K562 cells to identify 10 spatial compartmentalization states genome-wide relative to nuclear speckles, lamina, and putative associations with nucleoli. These SPIN states show novel patterns of genome spatial organization and their relation to other 3D genome features and genome function (transcription and replication timing). SPIN provides critical insights into nuclear spatial and functional compartmentalization....
PubMed:33446254