Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Defined chromosome structure in a minimal cell

ABSTRACT: Defined chromosome structure in a minimal cell

PROVIDER: PRJEB14019 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Defined chromosome structure in a minimal cell

Project description:Overall design Hi-C experiments were performed on untreated wild type cells at stationary and drug-treated cells (Novobiocin) of Mycoplasma Pneumoniae MPN129. We studied the chromosome organization of the genome-reduced bacterium, Mycoplasma pneumoniae, which has minimal genetic components and lacks several structural DNA-binding proteins. Platforms : Illumina HiSeq 2000 (Mycoplasma Pneumoniae MPN129)

2016-12-21 | E-MTAB-3721 | biostudies-arrayexpress

3D Chromosome Structure Can Reveal Stem Cell Signatures

Project description:3D Chromosome Structure Can Reveal Stem Cell Signatures

| PRJNA518890 | ENA

Single cell Hi-C reveals cell-to-cell variability in chromosome structure

Project description:Large-scale chromosome structure and spatial nuclear arrangement have been linked to control of gene expression and DNA replication and repair. Genomic techniques based on chromosome conformation capture assess contacts for millions of loci simultaneously, but do so by averaging chromosome conformations from millions of nuclei. Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes, to show that individual chromosomes maintain domain organisation at the megabase scale, but show variable cell-to-cell chromosome territory structures at larger scales. Despite this structural stochasticity, localisation of active gene domains to boundaries of territories is a hallmark of chromosomal conformation, affecting most domains in most nuclei. Single cell Hi-C data bridge current gaps between genomics and microscopy studies of chromosomes, demonstrating how modular organisation underlies dynamic chromosome structure, and how this structure is probabilistically linked with genome activity patterns. Mouse Th1 single-cell Hi-C maps were produced and paired-end sequenced. 10 single-cell samples and a multi-sample pool together with a population Hi-C sample are included.

2013-09-26 | E-GEOD-48262 | biostudies-arrayexpress

Single cell Hi-C reveals cell-to-cell variability in chromosome structure

2013-09-26 | GSE48262 | GEO

3D Chromosome Structure Can Reveal Stem Cell Signatures (ChIP-Seq)

Project description:3D Chromosome Structure Can Reveal Stem Cell Signatures (ChIP-Seq)

| PRJNA518892 | ENA

3D Chromosome Structure Can Reveal Stem Cell Signatures (RNA-Seq)

Project description:3D Chromosome Structure Can Reveal Stem Cell Signatures (RNA-Seq)

| PRJNA518893 | ENA

3D Chromosome Structure Can Reveal Stem Cell Signatures (Hi-C)

Project description:3D Chromosome Structure Can Reveal Stem Cell Signatures (Hi-C)

| PRJNA518894 | ENA

Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage

Project description:The International Stem Cell Initiative analyzed 127 human embryonic stem cell lines and 11 induced pluripotent cell lines, from 39 laboratories worldwide for genetic changes occurring during culture. Most cell lines were analyzed at an early and late passage. Population structure analysis from SNP detection revealed that the cell lines included representatives of all major ethnic groups. Most lines remained karyotypically normal, but there was a progressive tendency to acquire changes on prolonged culture, commonly affecting chromosomes 1, 12, 17 and 20. DNA methylation patterns changed but haphazardly with no link to time in culture. Structural variants (SVs), below the level of standard chromosome banding, determined from the SNP arrays, also appeared sporadically but no common variants related to culture were observed on chromosomes 1, 12 and 17. However, overlapping SV gains acquired in the chromosome 20q11.21 region during extended culture were identified in over 20% of the cell lines. Three genes within the minimal shared region, ID1, BCL2L1, and HM13, are expressed in human ES cells, with BCL2L1 a strong candidate for driving this culture adaptation of ES cells.

2011-11-12 | GSE33522 | GEO

Chromatin structure changes during cell reprogramming

Project description:3D structure of a 2.3 Mb region of human chromosome 12 (chr12: 6,140,000-8,460,000) containing GAPDH and NANOG loci in human IMR90 fibroblasts (hFibs) and fibroblast-derived human induced pluripotent stem cell (hiPSCs)

2021-06-30 | E-MTAB-10073 | biostudies-arrayexpress

The variation of 3D Chromosome Structure were tested during germline stem cell differentiation [HiC]

Project description:The variation of 3D Chromosome Structure were tested during germline stem cell differentiation [HiC]

| PRJNA688248 | ENA