Additional file 3: Table S2. HiC-Pro Quality Control Statistics

This data set provides raw energetic (MeV) particle data measured by the Heavy Ion Counter (HIC) instrument on the Galileo spacecraft. This data set contains both real-time and recorded data for all Jupiter orbits.

United States HIC: All Ages: PG: Private data was reported at 217,007.000 Person th in 2017. This records an increase from the previous number of 216,203.000 Person th for 2016. United States HIC: All Ages: PG: Private data is updated yearly, averaging 203,204.662 Person th from Mar 1999 (Median) to 2017, with 19 observations. The data reached an all-time high of 217,007.000 Person th in 2017 and a record low of 196,147.220 Person th in 2010. United States HIC: All Ages: PG: Private data remains active status in CEIC and is reported by US Census Bureau. The data is categorized under Global Database’s United States – Table US.G083: Health Insurance Coverage.

Hi-C and promoter capture Hi-C data for HT29 and LoVo. 2 replicates per cell line for the Hi-C. 3 replicates per cell line for the CHi-C.

This data set provides energetic (MeV) ion count rates and events measured by the Heavy Ion Counter (HIC) instrument on the Galileo spacecraft. These data are derived from high time resolution raw data that were recorded to tape and then played back later in the orbit. There are two basic types of data files associated with the full-rate reduced data: Detector Count Rates and Events (Pulse Heights).

Additional file 4: Table S3. Restriction Enzyme Sequences Used in the HiC-Pro Pipeline

The raw Hi-C metagenomic data were trimmed and aligned to the de-novo assemblies obtained from the paired shotgun metagenomes following the Hi-C kit manufacturer's recommendations (https://phasegenomics.github.io/2019/09/19/hic-alignment-and-qc.html). The contig-contig links or Hi-C links were quality-filtered for the identification of virus-host pairs.

This data set provides energetic (MeV) ion count rates and events measured by the Heavy Ion Counter (HIC) instrument on the Galileo spacecraft. The data are derived from the raw real-time science (RTS) data. There are two basic types of data files associated with the full-rate reduced data: Detector Count Rates and Events (Pulse Heights).

Additional file 17: Table S16. Map of Hi-C to ChIP-seq Signals

United States HIC: 35 to 44 Yrs data was reported at 40,046.000 Person th in 2016. This records an increase from the previous number of 40,005.300 Person th for 2015. United States HIC: 35 to 44 Yrs data is updated yearly, averaging 41,726.976 Person th from Mar 1999 (Median) to 2016, with 18 observations. The data reached an all-time high of 44,566.279 Person th in 2000 and a record low of 39,789.100 Person th in 2013. United States HIC: 35 to 44 Yrs data remains active status in CEIC and is reported by US Census Bureau. The data is categorized under Global Database’s USA – Table US.G082: Health Insurance Coverage.

This dataset contains chromosomal conformation capture data from fourteen samples (eleven tumor samples and three tumor derived cell lines). Libraries were prepared using the Illumina TruSeq LT sequencing adaptors. Sequencing was performed on the HiSeq X or NovaSeq platforms resulting in 28 FASTQ files.

This data set provides energetic (MeV) ion fluxes for a variety of different Z values (carbon, oxygen, sulfur) derived from the Heavy Ion Counter (HIC) instrument on the Galileo spacecraft. The data set includes all recorded intervals at Jupiter.

Hi-C is commonly used to study three-dimensional genome organization. However, due to the high sequencing cost and technical constraints, the resolution of most Hi-C datasets is coarse, resulting in a loss of information and biological interpretability. Here we develop DeepHiC, a generative adversarial network, to predict high-resolution Hi-C contact maps from low-coverage sequencing data. We demonstrated that DeepHiC is capable of reproducing high-resolution Hi-C data from as few as 1% downsampled reads. Empowered by adversarial training, our method can restore fine-grained details similar to those in high-resolution Hi-C matrices, boosting accuracy in chromatin loops identification and TADs detection, and outperforms the state-of-the-art methods in accuracy of prediction. Finally, application of DeepHiC to Hi-C data on mouse embryonic development can facilitate chromatin loop detection. We develop a web-based tool (DeepHiC, http://sysomics.com/deephic) that allows researchers to enhance their own Hi-C data with just a few clicks.

colon37 Hi-C datasets. 5 matrices corresponding to technical replicates, all given at three different resolutions (200 kb, 500kb, 1Mb) and for three different chromosomes (1, 7, 21). Original sequencing data are ENCODE data from a Hi-C experiment performed on a human colon sample (experiment accession: ENCSR295BDK), that include five technical replicates (sequencing runs). To obtain Hi-C matrices, raw sequencing reads of each technical replicate were processed using the nf-core/hic pipeline v1.2.2 on the assembly version GRCh38 of the human genome. ctcf 6 matrices corresponding to biological replicates at 100 kb resolution. Raw interaction counts of the six Hi-C matrices were directly downloaded from the GEO platform uwing the accession ID GSE168251 from NCBI. File list: GSM5133388_120min_no_a_rep1.cool.gz SM5133389_120min_no_a_rep2.cool.gz GSM5133390_120min_no_a_rep3.cool.gz GSM5133391_120min_with_a_rep1.cool.gz GSM5133392_120min_with_a_rep2.cool.gz GSM5133393_120min_with_a_rep3.cool.gz . Matrices in cool format were exported using the HiC-Pro text format by chromosome at 100 kb resolution.

Additional file 12: Table S11. Hi-C Loop Call Statistics for Mustache Loop Calling

HiC-bench task implementation. The table summarizes how the pipeline tasks are implemented, which are the requirements for their execution and how they are handled by the pipeline-master-explorer script. The first column lists all the tasks performed by the pipeline ranging from alignment to annotation. The second column lists the input directory required for each task while the third one lists the parameter files. Certain tasks depend on the reference genome (human or mouse), thus the genome assembly acts as split variable (column 4). In some tasks, replicates can be grouped using the group variable (column 5). Pairwise comparisons between replicates or samples are also allowed using tuples (column 6). The last column lists the full pipeline-master-explorer command for each pipeline task. (XLSX 10 kb)

Protein-Protein, Genetic, and Chemical Interactions for Nishiya N (2001):Hic-5-reduced cell spreading on fibronectin: competitive effects between paxillin and Hic-5 through interaction with focal adhesion kinase. curated by BioGRID (https://thebiogrid.org); ABSTRACT: Hic-5 is a paxillin homologue that is localized to focal adhesion complexes. Hic-5 and paxillin share structural homology and interacting factors such as focal adhesion kinase (FAK), Pyk2/CAKbeta/RAFTK, and PTP-PEST. Here, we showed that Hic-5 inhibits integrin-mediated cell spreading on fibronectin in a competitive manner with paxillin in NIH 3T3 cells. The overexpression of Hic-5 sequestered FAK from paxillin, reduced tyrosine phosphorylation of paxillin and FAK, and prevented paxillin-Crk complex formation. In addition, Hic-5-mediated inhibition of spreading was not observed in mouse embryo fibroblasts (MEFs) derived from FAK(-/-) mice. The activity of c-Src following fibronectin stimulation was decreased by about 30% in Hic-5-expressing cells, and the effect of Hic-5 was restored by the overexpression of FAK and the constitutively active forms of Rho-family GTPases, Rac1 V12 and Cdc42 V12, but not RhoA V14. These observations suggested that Hic-5 inhibits cell spreading through competition with paxillin for FAK and subsequent prevention of downstream signal transduction. Moreover, expression of antisense Hic-5 increased spreading in primary MEFs. These results suggested that the counterbalance of paxillin and Hic-5 expression may be a novel mechanism regulating integrin-mediated signal transduction.

This repository contains the phased HiC and related data reported in Liu et al. (submitted).Please refer to the Supplementary methods of the paper for an extensive description.Decompress the .tar.gz archive to find 4 main subfolders including:Supp1: Haplotypes calls (.haps format)Supp2: phased .hic maps (.maternal and .paternal, .hic format)Supp3: CNV callsSupp4: Calder subcompartment calls (unphased, maternal, paternal)

Protein-Protein, Genetic, and Chemical Interactions for Nishiya N (2002):Hic-5 interacts with GIT1 with a different binding mode from paxillin. curated by BioGRID (https://thebiogrid.org); ABSTRACT: Hic-5, a member of the paxillin family of adaptor molecules, is localized at focal adhesion and implicated in integrin-mediated signaling. Hic-5 and paxillin exhibit structural homology and share interacting factors, however, diverse functions are suggested for them. In this study, we carried out yeast two-hybrid screening to identify Hic-5 interacting factors using its LD3-4 region, which includes the Hic-5-specific amino acid sequence, as a bait. Through the screening, we identified GIT1, an Arf GTPase-activating protein, as a Hic-5 binding protein. The interaction of these two proteins was mediated by the LD3 motif of Hic-5 and the C-terminal region, which includes a paxillin-binding subdomain, of GIT1. Although GIT1 is known as a paxillin-binding protein, we only observed weak association of paxillin with GIT1 in the overexpression system. In contrast, Hic-5 firmly bound to GIT1 under the same conditions. In addition, the paxillin/GIT1 complex contained PIX, a guanine nucleotide exchange factor, whereas the Hic-5/GIT1 complex contained a smaller amount of PIX. These results suggested that paxillin and Hic-5 associate with GIT1 with different binding modes, and that the Hic-5 complex possesses static features compared with the paxillin complex, which contains both positive and negative regulators of GTPases involved in actin dynamics. Moreover, Hic-5-mediated inhibition of cell spreading was restored by co-expression of the C-terminal fragment of GIT1, which perturbs the interaction of Hic-5 with endogenous GIT1. Thus, it was demonstrated that Hic-5 and GIT1 interact functionally in addition to showing a physical association.

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