Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of biotin-labelled-miR190b pulldown

ABSTRACT: RNA-seq of biotin-labelled-miR190b pulldown

PROVIDER: PRJNA816541 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18336115_1.fastq.gz	Fastqsanger.gz
	SRR18336115_2.fastq.gz	Fastqsanger.gz
	SRR18336116_1.fastq.gz	Fastqsanger.gz
	SRR18336116_2.fastq.gz	Fastqsanger.gz
	SRR18336117_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 24

Similar Datasets

Comparing two approaches of miR-34a target identification, biotinylated-miRNA pulldown vs miRNA overexpression

Project description:Here we show that biotin-labelled miR-34a can be loaded to AGO2, and AGO2 immunoprecipitation can pulldown biotinylated miR-34a (Bio-miR pulldown). RNA-sequencing (RNA-seq) of the Bio-miR pulldown RNAs efficiently identified miR-34a mRNA targets, which could be verified with luciferase assays. In contrast to the approach of Bio-miR pulldown, RNA-seq of miR-34a overexpression samples had limited value in identifying direct targets of miR-34a. It seems that pulldown of 30 -Biotin-tagged miRNA can identify bona fide microRNA targets at least for miR34a.

2019-02-27 | GSE127211 | GEO

RNA-seq of biotin-labelled-miR190b pulldown

Project description:T-47d breast cancer cells were transfected in 6 test/control replicates with biotinylated miR-190b mimic or biotinylated mimic negative control by Qiagen. After 48h cells were lysed and miRNA:mRNA complexes were pulled-down by double precipitation. Firstly by pulling down Ago2 with Dynabeads G with rad Ago2 antibody and secondly via streptavidin coated magnetic beads. The precipitation was carried out according to manufacturer protocol. RNA from the eluted samples was then isolated using phenol-chloroform-isoamyl alcohol mixure and suspended in RNAse free water. This experiment was implemented to assess direct targets bound by miR-190b in the ER-positive breast cancer subtype T-47d.

2022-03-16 | GSE198723 | GEO

Chem-seq data from 5'-biotin-DRB-labelled human U2OS cells

Project description:Chem-seq data from 5'-biotin-DRB-labelled human U2OS cells

| PRJNA415843 | ENA

Chem-seq data from 5'-biotin-DRB-labelled human U2OS cells

Project description:Confluent U2OS cells were released to serum-free medium, and continued to grow for 36 h (Per2-dLuc peak), then added biotin-DRB (40uM) treatment for 0.5, then fixed the cells, harvested genomic DNA by Strepavidin agarose beads, and conducted hi-seq sequencing

2022-10-25 | GSE106193 | GEO

RNA pulldown target circGLS2

Project description:RNA pulldown target circGLS2

| PRJNA786500 | ENA

Biotin-13-cis retinoic acid pulldown LC-MSMS

Project description:We performed pulldown assays followed by mass-spectrometry analysis using biotin-tagged 13-cis retinoic acid to identify its binding targets in HeLa cells

2022-01-14 | PXD029579 | Pride

FoxP3 Pulldown-seq (Nucleosomal DNA)

Project description:FoxP3 Pulldown-seq (Nucleosomal DNA)

| PRJNA1018996 | ENA

biotin RNA pulldown assay of lnc-GD2H and mass spectrometry

Project description:Vectors carrying lnc-GD2H and antisense lnc-GD2H were linearized with the corresponding restriction enzymes to prepare template DNAs for in vitro transcription. Biotinylated RNAs were mixed with proteins extracted from C2C12 cells, followed by targeting of the RNAs with streptavidin beads. After SDS-PAGE following RNA pulldown, the differentially expressed proteins were enzymolyzed and used for MS analysis.

2021-05-18 | PXD025292 | Pride

Biotin-pgRNAWT or Biotin-pgRNAAUUUA to AUCUC RNA pulldown LC-MS/MS

Project description:The nuclear export of HBV RNAs allows the virus to synthesize its proteins through the translation machinery and replicate its genome through reverse transcription in the cytoplasm. However, the molecular mechanisms underlying this important process remain largely obscure. To illustrate this process, we took advantage of an unbiased HBV RNA-host protein interaction screen using a quantitative proteomics approach and identified embryonic lethal, abnormal vision, Drosophila-like 1 (ELAVL1) as a viral RNA binding partner. RNA scope and subcellular mRNA assays indicated that genetic and pharmaceutic inhibition of ELAVL1 inhibits HBV RNA nuclear export and suppresses viral replication in cell cultures. The observations of an HBV replication mouse model with ELAVL1 displayed similar results. RNA pulldown and RNA electrophoretic mobility shift assays revealed direct interaction between ELAVL1 and HBV pgRNA and confirmed AU-rich elements as the binding sites through site-directed mutagenesis of pgRNA. RNA-immunoprecipitation revealed that HBV RNAs associate with ELAVL1, which in turn binds to acidic leucine-rich nuclear phosphoprotein 32 family member A (ANP32A) and ANP32B. These interactions subsequently recruit CRM1. A nuclear RNase-targeted siRNA screen uncovered RNA exosome-mediated degradation of retardant HBV RNA after ELAVL1 or CRM1 knockdown. Further investigation revealed that ELAVL1 protects pgRNA from degradation. Notably, HBc deletion had no effect on pgRNA-CRM1 interaction and HBV RNA nuclear export. In summary, our work indicates that ELAVL1 functions both in HBV RNA stability and nucleocytoplasmic transport via the CRM1 nuclear export pathway.

2024-05-21 | PXD044015 | Pride

RNA-seq of metabolically labelled RNA by 4-thiouracil from mouse tissues

Project description:RNA-seq of metabolically labelled RNA by 4-thiouracil from mouse tissues

| PRJEB24362 | ENA