Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of mouse embryonic stem cells with knockout of Nhlrc2 gene or addition of FINCA disease causing NHLRC2 p.Asp148Tyr variant

ABSTRACT: RNA-seq of mouse embryonic stem cells with knockout of Nhlrc2 gene or addition of FINCA disease causing NHLRC2 p.Asp148Tyr variant

PROVIDER: PRJEB76623 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR13265653_1.fastq.gz	Fastqsanger.gz
	ERR13265653_2.fastq.gz	Fastqsanger.gz
	ERR13265654_1.fastq.gz	Fastqsanger.gz
	ERR13265654_2.fastq.gz	Fastqsanger.gz
	ERR13265655_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

PD-1 Knockout Engineered T Cells for Advanced Colorectal Cancer with MSI high expression

Project description:Interventions: experimental group :PD-1 Knockout Engineered T Cells Primary outcome(s): Number of participants with Adverse Events and/or Dose Limiting Toxicities as a Measure of Safety and tolerability of dose of PD-1 Knockout T cells using Common Terminology Criteria for Adverse Events (CTCAE v4.0) in patients Study Design: historical control

| 2662961 | ecrin-mdr-crc

Transcriptome profiling of CycG1-/- knockout, CycG2-/- knockout, and CycG1-/-CycG2-/- double knockout deficient mouse embryonic fibroblasts

Project description:Transcriptome profiling of CycG1-/- knockout, CycG2-/- knockout, and CycG1-/-CycG2-/- double knockout deficient mouse embryonic fibroblasts

| PRJNA316453 | ENA

Wild-type and nm1-knockout mouse embryonic fibroblasts

Project description:Wild-type and nm1-knockout mouse embryonic fibroblasts

| PRJNA817636 | ENA

Differences in metabolism in mouse embryonic fibroblasts (control vs SCF-beta-TrCP knockout)

Project description:Mouse embryonic fibroblasts were grown in DMED supplemented with 10%FBS. The same number of cells were plated in eight 6cm dishes. When the cells were ~70% confluent, four dishes received ethanol (carrier) and the other four received tamoxifen (1uM final) to induce knockout. The cells and media were harvested 4 days later. The media harvested from control and knockout dishes will be compared with the starting medium. The cells were washed with cold PBS twice while they are attached to the dishes. The whole dish with cells attached were immediately frozen in dry ice and wrapped with aluminum foil and stored at -80C.

2017-06-19 | ST000701 | MetabolomicsWorkbench

SIN3A Acetylation Complex - Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal

Project description:Sin3a is the central scaffold protein of the prototypical Hdac1/2 chromatin repressor complex, crucially required during early embryonic development for the growth of pluripotent cells of the inner cell mass. Here, we explore the endogenous composition of the Sin3a-Hdac complex in pluripotent embryonic stem (ES) and differentiated cells. To do this, we established an endogenous double immunoprecipitation strategy coupled with quantitative mass spectrometry (ENDIP-MS) allowing us to define the precise composition of the Sin3a complex in multiple cell types. We identify the Fam60a subunit as a key defining feature of a variant Sin3a complex present in ES cells, but not in differentiated cells. Fam60a co-occupies H3K4me3 positive promoters with Sin3a and is essential to maintain it on chromatin. Consistent with this, Fam60a depletion phenocopies the loss of Sin3a, leading to decreased proliferation, an extended G1-phase and the deregulation of genes associated with differentiation. Taken together, our data characterise Fam60a as an essential core subunit of a variant Sin3a complex in ES cells required to promote rapid proliferation and to prevent unscheduled differentiation.

2017-05-19 | PXD005464 | Pride

A Germline Heterozygous Dominant Negative IKZF2 Variant Causing Syndromic Primary Immune Regulatory Disorder and ICHAD

Project description:A Germline Heterozygous Dominant Negative IKZF2 Variant Causing Syndromic Primary Immune Regulatory Disorder and ICHAD

| PRJNA989151 | ENA

A Granulin Variant Causing Childhood Interstitial Lung Disease Responsive to anti-TNF-a Biologic Therapy

Project description:A Granulin Variant Causing Childhood Interstitial Lung Disease Responsive to anti-TNF-a Biologic Therapy

| PRJNA1140566 | ENA

Studies on a hydrocephalus-causing mutation on Trim71 [RNA-seq]

Project description:We studies on how a hydrocephalus-causing mutation (R783H) on mouse Trim71 alters transcriptomes in mouse embryonic stem cells

2022-11-04 | GSE196017 | GEO

A Germline Heterozygous Dominant Negative IKZF2 Variant Causing Syndromic Primary Immune Regulatory Disorder and ICHAD

Project description:Monogenic defects that impair the control of inflammation and tolerance lead to profound immune dysregulation, including autoimmunity and atopy. Studying these disorders reveals important molecular and cellular factors that regulate human immune homeostasis and identifies potential precision medicine targets. Here, we provide a detailed immunological assessment of a pediatric patient with a recently discovered syndrome causing Immunodysregulation, Craniofacial anomalies, Hearing impairment, Athelia, and Developmental delay (or ICHAD syndrome). The immunodysregulation resulted in autoimmune hemolytic anemia (AIHA) and atopic dermatitis. The patient carried a de novo germline heterozygous c.406+540_574+13477dup;p.Gly136_Ser191dup variant in IKAROS family zinc finger 2 (IKZF2), which encodes HELIOS. This variant led to reduced HELIOS protein expression and dominant interference of wild-type HELIOS-mediated repression of the IL2 promoter. Multi-parameter flow cytometric analyses of patient peripheral blood mononuclear cells revealed strongly impaired natural killer cell differentiation and function, and increased CD8+ T cell activation and cytokine secretion. Strikingly, patient CD4+ T cells were hyperactive, produced elevated levels of nearly all T helper (TH) cytokines, and readily proliferated in response to stimulation. Patient regulatory T cells (Tregs) developed normally but aberrantly produced high levels of many TH cytokines. Single-cell RNA sequencing revealed largely normal Tregs (albeit mostly memory), but naïve CD4+ T cells that were more enriched in genes related to activation, proliferation, metabolism, and TH differentiation. This work describes the immunological phenotype of one of the first reported cases of germline dominant negative HELIOS deficiency, expands our understanding of the pathogenesis of AIHA on a single cell level, and provides valuable insights into HELIOS function in a variety of lymphocyte subsets.

2025-04-29 | GSE236159 | GEO

Histone exchange sensors reveal variant specific dynamics in mouse embryonic stem cells

Project description:Eviction of histones from nucleosomes and their exchange with newly synthesized or alternative variants is a central mechanism shaping the epigenome. Here, we implemented a recently established sensor system that enables measuring genome-wide incorporation and exchange of canonical and non-canonical histone variants in mouse embryonic stem cells. While exchange of all measured variants scales with transcription, variant-specific patterns are associated with transcription elongation and Polycomb binding. We found considerable exchange rates of canonical H3.1 and H2B in heterochromatin and repeat elements where non-canonical H3.3 is stably incorporated but not exchanged. This unexpected association between H3.3 incorporation and the exchange of H3.1 and H2B is also evident in active promoters and enhancers, which we validated using HIRA knockout cells harboring the sensor system. The sensor system provides a powerful experimental framework with quantitative readout, facilitating functional studies of histone dynamics and epigenetic gene regulation in vivo.

2023-05-24 | GSE213076 | GEO

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