Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome

ABSTRACT: Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome

PROVIDER: PRJNA336566 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR4000660_1.fastq.gz	Fastqsanger.gz
	SRR4000660_2.fastq.gz	Fastqsanger.gz
	SRR4000670_1.fastq.gz	Fastqsanger.gz
	SRR4000670_2.fastq.gz	Fastqsanger.gz
	SRR4000680_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 56

Similar Datasets

Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome

Project description:Structural analysis of chromosome folding in vivo has been revolutionized by Chromosome Conformation Capture (3C) and related methods, which use proximity ligation to identify chromosomal loci in physical contact. We recently described a variant 3C technique, Micro-C, in which chromatin is fragmented to mononucleosomes using micrococcal nuclease, enabling nucleosome-resolution folding maps of the genome. Here, we describe an improved Micro-C protocol using long crosslinkers, termed Micro-C XL, which exhibits greatly increased signal to noise, and provides further insight into the folding of the yeast genome. We also find that signal to noise is much improved in Micro-C XL libraries generated from relatively insoluble chromatin as opposed to soluble material, providing a simple method to physically enrich for bona-fide long-range interactions. Micro-C XL maps of the budding and fission yeast genomes reveal both short-range chromosome fiber features such as chromosomally-interacting domains (CIDs), as well as higher-order features such as clustering of centromeres and telomeres, thereby addressing the primary discrepancy between prior Micro-C data and reported 3C and Hi-C analyses. Interestingly, comparison of chromosome folding maps of S. cerevisiae and S. pombe revealed widespread qualitative similarities, yet quantitative differences, between these distantly-related species. Micro-C XL thus provides a single assay suitable for interrogation of chromosome folding at length scales from the nucleosome to the full genome.

2016-09-13 | GSE85220 | GEO

Assaying 6xIAPP toxicity

Project description:Assaying 6xIAPP toxicity

| PRJNA411917 | ENA

Micro-C XL of Saccharomyces cerevisiae

Project description:Micro-C XL of Saccharomyces cerevisiae

| PRJNA943486 | ENA

Assaying RNA Structure with LASER-seq

Project description:Assaying RNA Structure with LASER-seq

| PRJNA451460 | ENA

Condensin-dependent chromatin condensation represses transcription globally during quiescence [Micro-C XL]

Project description:Quiescence is a stress-resistant state in which cells reversibly exit the mitotic cell cycle and suspend most cellular processes. Quiescence is essential for stem cell maintenance and its misregulation is implicated in tumor formation. One of the conserved hallmarks of quiescent cells, from Saccharomyces cerevisiae to humans, is highly condensed chromatin. Here, we use Micro-C XL to map chromatin contacts at single-nucleosome resolution genome-wide to elucidate mechanisms and functions of condensed chromatin in quiescent S. cerevisiae cells. We describe previously uncharacterized chromatin domains on the order of 10-60 kilobases that in quiescent cells are formed by condensin-mediated chromatin loops. Conditional depletion of condensin prevents chromatin condensation during quiescence entry and leads to widespread transcriptional de-repression. We further demonstrate that condensin-dependent chromatin compaction is conserved in quiescent human fibroblasts. We propose that condensin-dependent condensation of chromatin represses transcription throughout the quiescent cell genome.

2018-12-27 | GSE120605 | GEO

BCL-XL inhibition induces an FGFR4 mediated rescue response in colorectal cancer

Project description:The heterogeneous therapy response observed in colorectal cancer is in part due to cancer stem cells (CSCs) that resist chemotherapeutic insults. The anti-apoptotic protein BCL-XL plays a critical role in protecting CSCs from cell death, where its inhibition with high doses of BH3-mimetics can induce apoptosis. To identify pathways that can regulate sensitivity to BCL-XL inhibition, we screened a compound library for synergy with low dose BCL-XL inhibitor A-1155463 and reveal that FGFR4 inhibition effectively sensitizes to A-1155463 both in vitro and in vivo. Mechanistically, we identify a rescue response that is activated upon BCL-XL inhibition and leads to rapid FGF2 secretion and subsequent FGFR4-mediated post-translational stabilization of MCL-1. FGFR4 inhibition prevents MCL-1 upregulation and thereby sensitizes CSCs to BCL-XL inhibition. Altogether, our findings suggest a cell transferable induction of a FGF2/FGFR4 rescue response in CRC that is induced upon BCL-XL inhibition and leads to MCL-1 upregulation.

2021-12-22 | GSE159504 | GEO

Neurospora crassa strain:XL-ADAT

Project description:Neurospora crassa XL-ADAT Gene Expression Profiling - XL-ADAT_1 transcriptome

| PRJNA583843 | ENA

Neurospora crassa strain:XL-ADAT

Project description:Neurospora crassa XL-ADAT Gene Expression Profiling - XL-ADAT_2 transcriptome

| PRJNA583844 | ENA

Neurospora crassa strain:XL-ADAT

Project description:Neurospora crassa XL-ADAT Gene Expression Profiling - XL-ADAT_3 transcriptome

| PRJNA583845 | ENA

Silkworm scales LC-MS/MS amalysis raw data

Project description:To identify the cuticular proteins in developing wing scales of Bombyx mori, we performed LC-MS/MS analysis of dissoliving developing wing scales from Bombyx mori

2021-04-26 | PXD024365 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data