Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Estimating and predicting the resolution of HiC libraries

ABSTRACT: High resolution HiC libraries are usually lightly sequenced before investing in a deep sequencing. We modeled HiC resolution in function of the sequencing depth to predict accurately the resolution of any high resolution HiC library given a small sequnecing batch of the library. To test our tool, we used public datasets as well as a newly generated dataset using Arima kit on mouse purified rods photoreceptors.

ORGANISM(S): Mus musculus

PROVIDER: GSE152491 | GEO | 2021/11/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Estimating and predicting the resolution of HiC libraries

Project description:Estimating and predicting the resolution of HiC libraries

| PRJNA639530 | ENA

HiC data of the human oesophageal adenocarcinoma (EAC) cell lines OE19

Project description:This dataset consists of in situ HiC-seq data from a human oesophageal adenocarcinoma cell line (OE19). In total, the dataset includes 2 biological replicated samples. The Hi-C sample and library preparations were generated using Arima-HiC Kit (A510008, ARIMA Genomics) and Arima Library Prep module (A303011, ARIMA Genomics), respectively.

2023-02-20 | E-MTAB-12664 | biostudies-arrayexpress

Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals

Project description:Vertebrate ancestors had only cone-like photoreceptors. The duplex retina evolved in jawless vertebrates with the advent of highly photosensitive rod-like photoreceptors. Despite cones being the arbiters of high-resolution color vision, rods emerged as the dominant photoreceptor in mammals during a nocturnal phase early in their evolution. We investigated the evolutionary and developmental origins of rods in two divergent vertebrate retinae. In mice, we discovered genetic and epigenetic vestiges of short wavelength cones in developing rods and cell lineage tracing validated the genesis of rods from S-cones. Curiously, rods did not derive from S-cones in zebrafish. Our study illuminates several questions regarding the evolution of duplex retina and supports the hypothesis that, in mammals, the S-cone lineage was recruited via the Maf-family transcription factor NRL to augment rod photoreceptors. We propose that this developmental mechanism allowed the adaptive exploitation of scotopic niches during the nocturnal bottleneck early in mammalian evolution.

2016-06-21 | GSE74660 | GEO

Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals

2016-06-21 | GSE81953 | GEO

Recruitment of Rod Photoreceptors from Short Wavelength Sensitive Cones during the Evolution of Nocturnal Vision in Mammals

2016-06-21 | GSE81099 | GEO

Predicting the molecular complexity of sequencing libraries.

Project description:Predicting the molecular complexity of a genomic sequencing library is a critical but difficult problem in modern sequencing applications. Methods to determine how deeply to sequence to achieve complete coverage or to predict the benefits of additional sequencing are lacking. We introduce an empirical bayesian method to accurately characterize the molecular complexity of a DNA sample for almost any sequencing application on the basis of limited preliminary sequencing.

| S-EPMC3612374 | biostudies-literature

Ultrafine Mapping of Chromosome Conformation at hundred basepair resolution reveals regulatory genome architecture

Project description:The resolution limit of chromatin conformation capture methodologies (3Cs) has restrained their application in detection of fine-level chromatin structure mediated by cis-regulatory elements (CREs). Here we report two 3C-derived methods, Tri-4C and Tri-HiC, utilizing mult-restriction enzyme digestions capable of achieveing ultrafine genome digestion for targeted and global chromatin interaction mapping, respectively, at a one hundred basepair resolution. Tri-4C identified loops associated with CREs including those involving regulatory elements devoid of typical epigenomic marks, quantifatively revealing alterations in interaction networks underlying dynamic gene control. Tri-HiC successfully uncovers fine-gage enhancer:promoter (E:P) loops at genome-wide level, identifying > 20-fold more CRE loops than in situ HiC. In addition to refined loop detection, Tri-HiC also reveals interaction stripes and contact domain insulation from promoters and enhancers, revealing their loop extrusion behaviors resembling the topologically-associated domain (TAD) boundaries. Tri-4C and Tri-HiC provide robust approaches to achieve the high resolution interactome maps required for characterizing fine-gage regulatory chromatin interactions in analysis of development, homeostasis and disease.

2021-11-02 | GSE161014 | GEO

Predicting protein folds with fold-specific PSSM libraries.

Project description:Accurately assigning folds for divergent protein sequences is a major obstacle to structural studies. Herein, we outline an effective method for fold recognition using sets of PSSMs, each of which is constructed for different protein folds. Our analyses demonstrate that FSL (Fold-specific Position Specific Scoring Matrix Libraries) can predict/relate structures given only their amino acid sequences of highly divergent proteins. This ability to detect distant relationships is dependent on low-identity sequence alignments obtained from FSL. Results from our experiments demonstrate that FSL perform well in recognizing folds from the "twilight-zone" SABmark dataset. Further, this method is capable of accurate fold prediction in newly determined structures. We suggest that by building complete PSSM libraries for all unique folds within the Protein Database (PDB), FSL can be used to rapidly and reliably annotate a large subset of protein folds at proteomic level. The related programs and fold-specific PSSMs for our FSL are publicly available at: http://ccp.psu.edu/download/FSLv1.0/.

| S-EPMC3116844 | biostudies-literature

Promoter Capture-HiC in Ring1a KO and Ring1a/b dKO mouse ES cells

Project description:Genome organization influences transcriptional regulation by facilitating interactions between gene promoters and distal regulatory elements. To analyse distal promoter contacts mediated by the PRC1 complex we used Capture Hi-C (CHi-C) to enrich for promoter-interactions in a HiC library in Ring1a KO and Ring1a/b dKO mouse ES cells.

2015-08-01 | E-MTAB-3109 | biostudies-arrayexpress

Project description:Beaufortia pingi whole genome sequencing of HiC library

| PRJNA1068203 | ENA