Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ATAC-seq to Profile the Chromatin Accessibility in RBM22-silencing and Control Primary Cardiomyocytes

ABSTRACT: Purpose: The purpose of this study is to identify chromatin alterations regulated by RBM22. We performed ATAC-sequencing in primary cultured neonatal mouse cardiomyocytes transfected with control siRNA or Rbm22 siRNA. Methods: Cardiomyocytes were isolated from 1-day-old C57BL/6J mice and cultured in DMEM with 10% fetal bovine serum at 37°C in an atmosphere with 5% CO2. Cardiomyocytes were stained to confirm the expression of c-TnT. Cells with purity >97.5% were used for subsequent experiments. Cardiomyocytes were transfected with control siRNA or Rbm22 siRNA for 48 hours. Results: We identified regions of chromatin that were altered between cardiomyocytes transfected with the indicated siRNAs.

ORGANISM(S): Mus musculus

PROVIDER: GSE295696 | GEO | 2026/02/12

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Next Generation Sequencing Facilitates Quantitative Analysis of RBM22-silencing and Control Primary Neonatal Mouse Cardiomyocytes Transcriptomes

Project description:Purpose:The purpose of this study is to identify genes that are either activated or silenced in cardiomyocytes treated with siRNA targeting RBM22 (si-Rbm22) compared to control siRNA (si-Control). Gene expression differences between the two samples were identified using transcriptome profiling (RNA-seq) analysis. Methods: Primary neonatal mouse cardiomyocytes were isolated from neonatal C57BL/6J mice at postnatal day 1.Cardiomyocytes were stained to confirm the expression of c-TnT. Cells with purity >97.5% were used for subsequent experiments. Neonatal cardiomyocytes in primary culture were transfected with either siRNA targeting Rbm22 (si-Rbm22) or a non-targeting control siRNA (si-Control) for 48 h, of which RNA profiles were generated by deep sequencing using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome and identified numerous genes with significant mRNA variation between cardiomyocytes transfected with the indicated siRNAs.

2026-02-12 | GSE295695 | GEO

RBM22 CUT&Tag Profiling of Regenerative (P1) and Non-Regenerative (P8) Neonatal Mouse Cardiomyocytes

Project description:Purpose: To uncover the molecular mechanisms underlying RBM22-mediated neonatal heart regeneration, we performed Cleavage Under Targets and Tagmentation (CUT&Tag) analysis on regenerative and non-regenerative wild-type (WT) mouse cardiomyocytes over a 7-day period. Methods: Cardiomyocytes were isolated from postnatal day 1 (P1, regenerative) and postnatal day 8 (P8, non-regenerative) mice, and cultured in DMEM supplemented with 10% fetal bovine serum at 37°C in a 5% CO₂ atmosphere. Cells were stained to confirm the expression of c-TnT, and only those with purity >97.5% were used for subsequent experiments.Results: We carried out a CUT&Tag assay using antibody against RBM22 and found the global influence of RBM22 in regulating genes in transcription regulatory regions of key genes involved in proliferative cardiomyocyte effector function.

2026-02-12 | GSE295697 | GEO

ATAC-seq Profiling of Adult Mouse Cardiomyocytes Treated with AAV9-cTnT-Rbm22 in MI Model

Project description:Purpose: The purpose of this study was to identify chromatin alterations regulated by RBM22 in adult mouse cardiomyocytes (AMCMs) after myocardial infarction (MI). We performed ATAC sequencing on AMCMs isolated from mice post-MI that were infected with either AAV9-cTnT-GFP (control viral vector, AAV9-Control) or AAV9-cTnT-Rbm22-GFP (AAV9-Rbm22). Methods: 8-week-old C57BL/6J mice underwent permanent ligation of the left anterior descending (LAD) coronary artery, followed immediately by intramyocardial injection of either AAV9-Control or AAV9-Rbm22 at the infarct border zone. Adult cardiomyocytes were isolated post-MI using the Langendorff perfusion method. Results: We identified differentially altered chromatin accessibility regions between adult cardiomyocytes injected with the indicated viral vectors post-MI.

2026-02-12 | GSE311241 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Bone Marrow-Derived Macrophages Transcriptomes for Acly-E14 siRNA effects

Project description:Purpose: The purpose of this study is to detect activated or silenced genes during bone marrow derived macrophages (BMDMs) transfected with control siRNA or Acly-E14 siRNA. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. BMDMs were transfected with control siRNA or Acly-E14 siRNA. 48 hour later, they were stimulated with LPS (100ng/ml) for 4 hours, of which RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between BMDMs transfected with the indicated siRNAs.

2024-11-06 | GSE240188 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Bone Marrow-Derived Macrophages Transcriptomes for Acly-E14 ASO effects

Project description:Purpose: The purpose of this study is to detect activated or silenced genes during bone marrow derived macrophages (BMDMs) transfected with control siRNA or Acly-E14 siRNA. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse BMDMs were generated from bone marrow cells in RPMI-1640 medium with recombinant mouse M-CSF (20ng/ml). BMDMs were stained to confirm the surface expression of CD11b and F4/80. Cells with purity >97.5% were used for subsequent experiments. BMDMs were transfected with control ASO or Acly-E14 ASO. 48 hour later, they were stimulated with LPS (100ng/ml) for 4 hours, of which RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between BMDMs transfected with the indicated ASOs.

2024-11-06 | GSE272304 | GEO

Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability [C3'-seq]

Project description:Splicing factors are vital for the regulation of RNA splicing, but the underlying molecular mechanisms of their involvement in transcriptional processes remain poorly understood. Here, we describe a direct role of splicing factor RBM22 in coordinating multiple steps of RNA Polymerase II (RNAPII) transcription in human cells. The RBM22 protein widely occupies the RNAPII-transcribed gene locus in the nucleus. Loss of RBM22 promotes RNAPII pause release, reduces elongation velocity and provokes transcriptional readthrough genome-wide, coupled with downstream-of-gene (DoG) transcript production and genome instability. RBM22 preferentially binds to the hyperphosphorylated, transcriptionally engaged RNAPII and coordinates its dynamics by regulating the homeostasis of the 7SK-P-TEFb complex and the association between RNAPII and SPT5 at the chromatin level. Our results uncover the multifaceted role of RBM22 in orchestrating the transcriptional program of RNAPII, and provide evidence implicating a splicing factor in both RNAPII elongation kinetics and termination control.

2024-03-10 | GSE220317 | GEO

Splicing Factor RBM22 Broadly Affects RNA Polymerase II 5' Pausing, Elongation Rate and Termination and Prevents Genome Instability [ChIP-seq]

2024-03-10 | GSE220316 | GEO

Loss of TET2 Impairs Endothelial Angiogenesis via Downregulating STAT3 Target Genes

Project description:To investigate the role of TET2 in HUVECs under hypoxia, HUVECs were exposed to an atmosphere of 1% oxygen, 5% CO2 and 94% N2 for 48 h, in which TET2 had been knocked down by siRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of HUVECs transfected with control siRNA or TET2 siRNA.

2023-01-25 | GSE200080 | GEO

RNA sequencing analysis for differentially expressed genes in neonatal rat cardiomyocytes following knockdown of transcription factor Vezf1

Project description:We performed a set of sequencing experiments to identify the targets of Vascular endothelial zinc finger 1 (Vezf1) in neonatal rat cardiomyocytes. We compared a set of control samples to samples transfected with Vezf1 siRNA by high throughput sequencing. Vascular endothelial zinc finger 1 (Vezf1) siRNA was transfected into the neonatal rat ventricular cardiomyocytes for 24h and thereafter the cells were incubated in serum free medium for 48h.

2019-11-30 | E-MTAB-7124 | biostudies-arrayexpress

Transcriptional effects of siRNA-mediated MAFB knockdown on SARS-CoV-2-infected human M-CSF and GM-derived macrophages.

Project description:To investigate the MAFB-dependent genes in the SARS-COV-2 infection on human macrophages, we generated M-CSF and GM-CSF-dependent monocyte-derived macrophages in which MAFB has been knocked down by siRNA and then infected with SARS-CoV-2. Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 for 6 days in the presence of GM-CSF or M-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were transfected with MAFB-specific siRNA or control siRNA, kept in culture for 6 hours, and then were exposed to SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1) or uninfected. After 36 hours, cells were lysed and RNA isolated for transcriptional analysis. We performed gene expression profiling analysis using data obtained from RNA-seq of 3 different donors.

2024-02-08 | GSE224131 | 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