Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bulk RNA sequencing of E14.5 embryonic hearts from cardiomyocyte-specific Cul3 conditional-knockout and control mice

ABSTRACT: To define transcriptional changes at E14.5 in the Cul3 conditional-knockout study, poly(A)-enriched RNA from embryonic cardiac tissue was profiled in three control (CTL) libraries and three Cul3 conditional-knockout (CKO) libraries. This GEO submission contains the six libraries used for the reported CTL-versus-CKO comparison. Reads were generated as 150-bp paired-end data. The deposit provides sample-demultiplexed FASTQ files, a complete unfiltered six-sample gene-count matrix, and six-sample-only DESeq2 results with normalized counts.

ORGANISM(S): Mus musculus

PROVIDER: GSE344680 | GEO | 2026/08/31

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Knockdown of CUL3 and PTEN in A549 lung adenocarcinoma cells

Project description:Non-small cell lung cancers (NSCLCs) harbor thousands of passenger events that hide genetic drivers. Even highly recurrent events in NSCLC, such as mutations in PTEN, EGFR, KRAS, and ALK, are only detected in, at most, 30% of patients. Thus, many unidentified low-penetrant events are causing a significant portion of lung cancers. To detect low-penetrance drivers of NSCLC a forward genetic screen was performed in mice using the Sleeping Beauty (SB) DNA transposon as a random mutagen to generate lung tumors in a Pten deficient background. SB mutations coupled with Pten deficiency were sufficient to produce lung tumors in 29% of mice. Pten deficiency alone, without SB mutations, resulted in lung tumors in 11% of mice, while the rate in control mice was ~3%. In addition, thyroid cancer and other carcinomas as well as the presence of bronchiolar and alveolar epithelialization in mice deficient for Pten were also identified. Analysis of common transposon insertion sites identified 76 candidate cancer driver genes. These genes are frequently dysregulated in human lung cancers and implicate several signaling pathways. Cullin3 (Cul3), a member of an ubiquitin ligase complex that plays a role in the oxidative stress response pathway, was identified in the screen and evidence demonstrates that Cul3 functions as a tumor suppressor HumanHT-12 v4 Expression BeadChip Kit for human A549 lung adenocarcinoma cells with CUL3, PTEN, CUL3 and PTEN or no knockdown. A549 cells were stably transfected under Puromycin or Hygromycin selection to knockdown PTEN (SA Biosystems) or CUL3 (Open Biosystems) shRNAs. RNA was extracted in triplicate from each condition and used for microarray

2015-05-15 | E-GEOD-68869 | biostudies-arrayexpress

Bulk RNA sequencing of E14.5 embryonic hearts from cardiomyocyte-specific Cul3 conditional-knockout and control mice

Project description:Bulk RNA sequencing of E14.5 embryonic hearts from cardiomyocyte-specific Cul3 conditional-knockout and control mice

| PRJNA1516559 | ENA

Knockdown of CUL3 and PTEN in A549 lung adenocarcinoma cells

2015-05-15 | GSE68869 | GEO

Metabolic Reprogramming in Tumor-Associated Macrophages during Murine Hepatocellular Carcinoma Progression

Project description:<p>To investigate the impact of Wdr4 on the metabolic reprogramming of tumor-associated macrophages (TAMs) in hepatocellular carcinoma (HCC), we established an orthotopic HCC model in Wdr4-f/f and Wdr4 conditional knockout (Wdr4-cKO) mice. TAMs were subsequently isolated via flow cytometry-based cell sorting. Untargeted metabolomics analysis was performed to identify metabolic alterations in TAMs associated with Wdr4 deficiency.</p>

2025-09-28 | MTBLS12764 | MetaboLights

Chromatin Remodeling Inactivates Activity Genes and Regulates Neural Coding

Project description:Activity-dependent transcription influences neuronal connectivity, but the roles and mechanisms of inactivation of activity-dependent genes have remained poorly understood. Genome-wide analyses in the mouse cerebellum revealed that the nucleosome remodeling and deacetylase (NuRD) complex deposits the histone variant H2A.z at promoters of activity-dependent genes, thereby triggering their inactivation. Purification of translating mRNAs from synchronously developing granule neurons (Sync-TRAP) showed that conditional knockout of the core NuRD subunit Chd4 impairs inactivation of activity-dependent genes when neurons undergo dendrite pruning. Chd4 knockout or expression of NuRD-regulated activity genes impairs dendrite pruning. Imaging of behaving mice revealed hyperresponsivity of granule neurons to sensorimotor stimuli upon Chd4 knockout. Our findings define an epigenetic mechanism that inactivates activity-dependent transcription and regulates dendrite patterning and sensorimotor encoding in the brain. One or two replicates of the histone modifications (H3K27me3 and H2A.z), total histone proteins (H2A.z and H3), and ATPase Chd4 using postnatal day 22 cerebella from wild type (WT) or Chd4 conditional knockout (cKO) mice were examined using libraries prepared with the Illumina ChIP-Seq DNA Sample Prep Kit. Four replicates of total RNA were extracted from postnatal day 27-28 cerebella from rotarod-trained or control homecage mice, or Chd4 cKO or WT mice using Trizol and reverse-transcribed with oligo-dT priming. Three replicates of immunoprecipitated Sync-TRAP RNA or the input control using postnatal day 12 Chd4 cKO or WT cerebella were purified and amplified with Ovation RNA-Seq System V2 (NuGEN). All samples were sequenced on the Illumina HiSeq 2000 platform.

2016-07-18 | E-GEOD-83253 | biostudies-arrayexpress

LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis SW480 [RNA-Seq]

Project description:The lncRNA EPR (a.k.a BC030870) is highly enriched in the gastrointestinal tract in mice and, more specifically, in the large intestine. We generated conditional EPR knock-out in large intestine e and analyzed genome-wide the gene expression changes by RNA-Seq. Total RNA was extracted from the proximal colon of six control (EPR fl/fl) and six knock-out (EPR cKO) mice. Libraries were constructed and sequenced. Results indicate that EPR knock-out predominantly leads to down-regulation of genes implicated in mucus biogenesis. These results help in explaining the phenotype displayed by EPR cKO mice that is characterized by higher susceptibility to intestinal inflammation and cancer formation.

2023-03-28 | GSE219181 | GEO

LncRNA EPR transcriptional activity controls intestinal mucus and prevents susceptibility to inflammation and tumorigenesis [RNA-seq]

2023-03-28 | GSE218994 | GEO

RNA-seq comparing the WT mouse hearts versus Dhx36 cKO hearts

Project description:This experiment aimed to investigate the transcriptional role of G4 resolvase Dhx36 in the adult mouse heart. We compared three pools of wild-type (WT) mouse hearts with three pools of Dhx36 conditional knockout (cKO) hearts. In the mutant mice, Dhx36 was conditionally deleted in cardiomyocytes using the Myh6-cre transgenic line. Each of the six pools was created using RNA extracted from 3-5 hearts from mice aged approximately 21 days. The cKO mice developed dilated cardiomyopathy and began experiencing sudden death at 40 days old, with no mutants surviving beyond 5 months.

2024-09-15 | E-MTAB-14440 | biostudies-arrayexpress

Chromatin remodeling BAF155 subunit regulates the genesis of basal progenitors in developing cortex

Project description:We have analyzed gene expression differences between control, BAF155 conditional knockout (cKO) and Pax6 cKO embryonic cortices at E15.5.

2018-05-11 | GSE114351 | GEO

Gene expression in the mouse embryonic small intestine in the presence or absence of E-cadherin

Project description:Gene expression was compared between E18.5 E-cadherin conditional knockout (cKO) small intestine and E18.5 control mouse small intestine. E18.5 mouse small intestine was collected from control and E-cadherin conditional knockout mice. RNA was prepared. Affymetrix Mouse Gene 1.0 gene arrays were used to interrogate gene expression. Data was analyzed using dChip software.

2012-02-28 | E-GEOD-31771 | biostudies-arrayexpress

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