Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Formaldehyde-fixed RNA-Immunoprecipitation (fRIP for heterogenous ribonucleoprotein K (hnRNP K)

ABSTRACT: Formaldehyde-fixed RNA-Immunoprecipitation (fRIP for heterogenous ribonucleoprotein K (hnRNP K)

PROVIDER: PRJNA522053 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8569440.fastq.gz	Fastqsanger.gz
	SRR8569441.fastq.gz	Fastqsanger.gz
	SRR8569436.fastq.gz	Fastqsanger.gz
	SRR8569437.fastq.gz	Fastqsanger.gz
	SRR8569438.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Formaldehyde-fixed RNA-Immunoprecipitation (fRIP for heterogenous ribonucleoprotein K (hnRNP K)

Project description:fRIP experiments were performed in OCI-AML3 cells to identify transcripts that bind to hnRNP K.

2019-05-01 | GSE126479 | GEO

Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions

Project description:Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions

| PRJNA716345 | ENA

LCDR maintains the integrity of lysosomal membrane by hnRNP K-stabilized LAPTM5 transcript and promotes cell survival

Project description:Lysosome plays important roles in cellular homeostasis and its dysregulation is associated with cancer. However, the regulation and underlying mechanism of lysosome in cancer survival remain incompletely understood. Here, we reveal a role for a histone acetylation-regulated long non-coding RNA termed as lysosome cell death regulator (LCDR) in lung cancer cell survival, knockdown of which promotes apoptosis. Mechanistically, LCDR binds to heterogenous nuclear ribonucleoprotein K (hnRNP K) to regulate the stability of lysosomal-associated protein transmembrane 5 (LAPTM5) transcript that maintain integrity of lysosomal membrane. Consequently, knockdown of LCDR, hnRNP K or LAPTM5 promotes lysosomal membrane permeabilization and lysosomal cell death-mediated apoptosis. LAPTM5 overexpression or cathepsin B inhibitor partially restores the effects of this axis on lysosomal cell death. Clinically, LCDR/hnRNP K/LAPTM5 are upregulated in lung cancer tissues and coexpression of this axis shows the increased diagnostic value for lung cancer. These findings shed light on LCDR/hnRNP K/LAPTM5 as potential therapeutic targets and targeting lysosome is a promising strategy in cancer treatment.

2021-05-05 | GSE173849 | GEO

Expression signatures of human HeLa cells with RNAi targetting A1 hnRNP, FUS, H hnRNP and p68-DDX5

Project description:Transcription profiling of human HeLa cells (cervical cancer cell line) transfected with a plasmid expressing shRNAs cloned into the pSuper expression vector compared to emprty vector negative controls for transfection. Four different RNA interference treatments targetted: A1 hnRNP (HNRNPA1, Heterogeneous nuclear ribonucleoprotein A1); FUS (fusion gene, involved in t(12;16) in malignant liposarcoma); H hnRNP (HNRNPH1); and p68 helicase (DDX5, DEAD (Asp-Glu-Ala-Asp) box polypeptide 5). Keywords: genetic modification

2008-08-20 | GSE12058 | GEO

Muscle Developmental Defects in Heterogeneous Nuclear Ribonucleoprotein A1 Knockout Mice

Project description:Transcriptome analysis of total RNA samples from heart tissue of knockout mice Alternative splicing is the main mechanism to increase protein diversity from an mRNA. Heterogeneous ribonucleoprotein (hnRNP) family members are vital regulators of alternative splicing. The hnRNP A1 is the most well-known protein in this family, but its role in embryonic development is not well understood. We generated hnRNP A1 knockout mice to study the function of hnRNP A1 in vivo. The hnRNP A1-depleted mice showed embryonic lethality because of muscle developmental defects. In a previous study, cellular hnRNP A2/B1 was reported to be capable of compensating for the expression of hnRNP A1. However, this phenomenon did not occur in the hnRNP A1 heterozygous mice in vivo. We demonstrated that hnRNP A1 regulated muscle-related genes expression and alternative splicing. In summary, our data demonstrated that hnRNP A1 plays a critical role in embryonic muscle development. Understanding the effects of hnRNP A1 in vivo may help to define the function of hnRNP A1 in alternative splicing.

2016-12-05 | GSE79076 | GEO

Aurora B phosphorylates hnRNP U/SAF-A to facilitate XIST RNA removal from the inactive X chromosome during mitosis

Project description:We show that Aurora-B phosphorylates heterogeneous nuclear ribonucleoprotein U (hnRNP U) in the SAP domain to dissociate hnRNP U from chromatin during mitosis. We use RNA-seq to show that hnRNP U associates with hundreds of mRNAs and lncRNAs during interphase and mitosis.

2020-09-02 | GSE87200 | GEO

Analysis of RNA quantitation in formaldehyde-fixed cells

Project description:Fluorescence-activated cell sorting (FACS) is a sensitive and valuable technique to characterize cellular subpopulations and great advances have been made using this approach. Cells are often fixed with formaldehyde prior to the sorting process to preserve cell morphology and maintain the expression of surface molecules, as well as to ensure safety in the sorting of infected cells. It is widely recognized that formaldehyde fixation alters RNA and DNA structure and integrity, thus analyzing gene expression in these cells has been difficult. We therefore examined the effects of formaldehyde fixation on the stability and quantitation of nucleic acids in cell lines, primary leukocytes and also cells isolated from SIV-infected pigtailed macaques. We developed a method to extract RNA from fixed cells that yielded the same amount of RNA as our common method of RNA isolation from fresh cells. Quantitation of RNA by RT-qPCR in fixed cells was not always comparable with that in unfixed cells. In comparison, when RNA was measured by the probe-based NanoString system, there was no significant difference in RNA quantitation. In addition, we demonstrated that quantitation of proviral DNA in fixed cells by qPCR is comparable to that in unfixed cells when normalized by a single-copy cellular gene. These results provide a systematic procedure to quantitate gene expression in cells that have been fixed with formaldehyde and sorted by FACS.

2013-09-09 | GSE50690 | GEO

Metastasis-repressive CircRNA MASCOT Regulates Distribution of the Splicing Factor hnRNP M

Project description:Alternative splicing (AS) diversifies the transcriptome complexity and is usually hijacked by cancer cells. Here, we identified heterogeneous nuclear ribonucleoprotein M (hnRNP M) as an indispensable contributor to EMT-related AS reprogramming, whose sub-nuclear distribution of hnRNP M is altered in metastatic tumors. Upon TGFβ stimulation, hnRNP M trends to disassociate with a circRNA called MASCOT (hnRNP M-ASsociated Circular RNA Of TGFβ) that demonstrated an impressive inhibitory effect on EMT process and tumor metastasis. Mechanistically, the anti-metastatic effect of MASCOT is attributed to not only its competition with U2 RNA splicing factors to recruit hnRNP M in the nucleoplasm, but also the anchorage of hnRNP M with nucleolin into the nucleolus to cause a temporospatial separation of hnRNP M from spliceosome. Moreover, the correlation between MASCOT expression and hnRNP M sub-nuclear localization was validated in clinical specimens. Our study deciphers the regulatory codes controlling AS networks and highlights MASCOT as a promising therapeutic to treat metastasis.

2022-09-20 | GSE213677 | GEO

Metastasis-repressive CircRNA MASCOT Regulates Distribution of the Splicing Factor hnRNP M

2022-09-10 | GSE165576 | GEO

40S hnRNP particles are a novel class of nuclear biomolecular condensates

Project description:Heterogenous nuclear ribonucleoproteins (hnRNPs) are abundant proteins implicated in various steps of RNA processing that assemble on nuclear RNA into larger complexes termed 40S hnRNP particles. Despite their initial discovery 55 years ago, our understanding of these intriguing macromolecular assemblies remains limited. We biochemically purified native 40S hnRNP particles and determined their complete protein composition by label-free quantitative mass spectrometry, identifying A-group and C-group hnRNPs as the major protein constituents.

2022-05-30 | PXD031677 | 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