Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA-seq]

ABSTRACT: Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA-seq]

PROVIDER: PRJNA1151638 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR30355362_1.fastq.gz	Fastqsanger.gz
	SRR30355362_2.fastq.gz	Fastqsanger.gz
	SRR30355363_1.fastq.gz	Fastqsanger.gz
	SRR30355363_2.fastq.gz	Fastqsanger.gz
	SRR30355364_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [bulkRNA-seq]

Project description:Bulk RNA sequencing analyses of whole kidney marrow tissue isolated from wild type and rad21 heterozygous mutant adult zebrafish.

2024-11-03 | GSE275536 | GEO

Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA-seq]

Project description:Single cell transcriptome analyses of whole kidney marrow cells isolated from wild type and rad21 heterozygous mutant adult zebrafish.

2024-11-03 | GSE275537 | GEO

Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA-seq]

Project description:Expression profiling of whole kidney marrow cells derived from wild type and rad21 heterozygous mutant adult zebrafish [scRNA-seq]

| PRJNA1151637 | ENA

Single-cell omics sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish

Project description:The transcription factor GATA2 plays a major role in the generation and maintenance of the hematopoietic system. In humans, heterozygous germline mutations in GATA2 often lead to a loss of function of one allele, causing GATA2 haploinsufficiency. In mice, Gata2 has an essential regulatory function in hematopoietic stem cell (HSC) generation and maintenance. However, whereas Gata2-null mice are lethal at embryonic day (E) 10.53, Gata2 heterozygous (Gata2+/-) mice survive to adulthood with normal blood values. However, mouse models thus emerged as a useful source to identify the function of GATA2 in HSC generation and fitness, they leave the mechanisms causing the different aspects of GATA2 deficiency syndrome largely undiscovered. Zebrafish have the advantage of having two GATA2 orthologues; Gata2a and Gata2b. Gata2a is expressed predominantly in the vasculature and is required for programming of the hemogenic endothelium. Gata2b is expressed in hematopoietic stem/progenitor cells (HSPCs) and homozygous deletion (gata2b-/-) redirects HSPCs differentiation bias, thus mimicking one of the GATA2 haploinsufficiency phenotypes found in patients. But patients carry heterozygous rather than homozygous GATA2 mutations, we specifically focused on how heterozygous Gata2b mutations could be mechanistically linked to erythro-myelodysplasia, a major clinical hallmark of GATA2 patients. To investigate the mechanisms of heterozygous GATA2 mutation caused GATA2 deficiency syndrome, we created a heterozygous gata2b mutation zebrafish model and sorted the entire progenitor and HSPC population including the lymphoid population from kidney marrow (KM) of WT and mutated zebrafish based on the scatter profile of flow cytometry for single-cell RNA (scRNA) sequencing.

2024-11-05 | E-MTAB-14075 | biostudies-arrayexpress

Single-cell ATAC sequencing of kidney marrow cells from heterozygous gata2b mutated and wild type zebrafish

2024-11-05 | E-MTAB-14076 | biostudies-arrayexpress

Expression data from zebrafish embryos homozygous mutant for the cohesin subunit Rad21

2009-10-30 | GSE18795 | GEO

Transcription profiling of zebrafish embryos homozygous mutant for the cohesin subunit Rad21

Project description:Rad21 is a subunit of cohesin. The main function of cohesin is to hold replicated chromosomes together until cells divide, but it also plays a role in gene expression. To find out which genes might be regulated by cohesin, a study was conducted to look for global changes in gene expression in zebrafish embryos lacking cohesin component Rad21. The zebrafish Rad21 mutant used for expression analysis was rad21nz171, an allele isolated in a forward genetic screen for regulators of runx1. Experiment Overall Design: RNA from rad21nz171 mutant and wild type zebrafish embryos collected at 24 hours post-fertilization (h.p.f.) and 48 h.p.f. was hybridized to Affymetrix microarrays (Gene Chip zebrafish genome arrays cat. no. 900488). Four pools of 50 embryos for each genotype and time point were used as the RNA source, and RNA from each pool was hybridized independently such that the experiment had four biological replicates.

2009-11-10 | E-GEOD-18795 | biostudies-arrayexpress

Genome-wide mapping of Rad21 binding sites and gene expression profiling in wild type mouse small intestinal epithelial crypts and Apc Min adenomas

Project description:To investigate the role of RAD21 in the transcriptional regulation of global gene expression at early stage of colorectal cancer developments, we peformed the genome-wide analysis to map genomic regions bound by Rad21 in normal small testinal crypts and tumors (adenomas) harvested from Apc Min/+ mice using ChIP-seq. ChIP-seq naalysis identified high confidence RAD21 binding sites unique to normal crypts or adenomas, as well as those common to both tissues. We further performed RNA-seq to profile the changes in gene expression from normal WT crypts to adenomas at the very early stage of adenomagenesis in the context of Rad21 heterozygous loss. mRNA profiles of normal small intestinal crypts (WT) and adenomas from Apc Min/+ and Apc Min/+:Rad21+/- double mutant mouse; Mapping of Rad21 genomic binding sites in normal intestinal crypts (WT) and Apc Min/+ adenomas

2014-10-31 | E-GEOD-59283 | biostudies-arrayexpress

Transcriptional profiling of rag1 deficient (rag1-/-) and rag1 heterozygous (rag1+/-) zebrafish kidney and intestine

Project description:Four dual hybridizations of rag1 deficient (rag1-/-) and rag1 heterozygous (rag1+/-) zebrafish cRNAs from kidney and intestine. Keywords: Gene knockout

2009-01-05 | GSE12655 | GEO

Rad21-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation

Project description:MTD project_description Inflammation and decreased stem cell function characterize organism aging, yet the relationship between these factors remains incompletely understood. This study shows that aged hematopoietic stem and progenitor cells exhibit increased ground-stage NF-κB activity, which enhances their responsiveness to undergo differentiation and loss of self-renewal in response to inflammation. The study identifies Rad21/cohesin as a critical mediator of NF-κB signals, by increasing chromatin accessibility of inter-/intra-genic and enhancer regions. Rad21/NF-κB are required for normal differentiation, but limit self-renewal of hematopoietic stem cells (HSCs) during aging and inflammation in an NF-κB dependent manner. HSCs from aged mice fail to downregulate Rad21/cohesin and inflammation/differentiation inducing signals in the resolution phase after acute inflammation. and The inhibition of cohesin/NF-κB is sufficient to revert the hypersensitivity of aged HSPCs to inflammation-induced differentiation. During aging, myeloid-biased HSCs with disrupted and naturally occurring reduced expression of Rad21/cohesin are increasingly selected over lymphoid-biased HSCs. Together, Rad21/cohesin mediated NF-κB signaling limits HSPC function during aging and selects for cohesin deficient HSCs with myeloid skewed differentiation.

2018-11-28 | PXD011537 | 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