Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: RNA-biotin based pull down assay with Hela Nuclear Extract followed by RNA-seq

PROVIDER: PRJNA384324 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5482375.fastq.gz	Fastqsanger.gz
	SRR5482376.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

RNA-biotin based pull down assay with polyA site (PAS) RNA substrates in Hela Nuclear Extract followed by RNA-seq to discover trans-acting RNA molecules involved in mRNA 3’ processing

Project description:RNA-biotin based pull down assay with polyA site (PAS) RNA substrates in Hela Nuclear Extract followed by RNA-seq to discover trans-acting RNA molecules involved in mRNA 3’ processing

| PRJEB19274 | ENA

RNA-biotin based pull down assay with Hela Nuclear Extract followed by RNA-seq

Project description:We aimed to discover trans-acting RNA molecules involved in mRNA 3’ processing. We reasoned that, if there exist such functional RNAs, they must directly associate with the key machinery responsible for mRNA 3’ processing. Therefore, it would be of great value to comprehensively identify RNAs interacting with pre-mRNA 3’ processing complex. To this goal, we took advantage of previously well-characterized system combined with high-throughput sequencing to investigate the target RNAs at the transcriptomic level. Briefly, we used polyA site (PAS) RNA substrates, SV40 late (SVL), and corresponding control RNAs with point mutation (U to C) at the highly conserved cis-element AAUAAA. RNA substrates were first biotinylated at the 3’ end, and then bound to the streptavidin magnetic beads. After incubation with Hela Nuclear Extract (NE) under polyadenylation condition, the two wild type RNA substrates could specifically recruit mRNA 3’ processing factors in NE for complex assembly. The purification of the protein complex and its interacting RNAs were performed using biotin-streptavidin pull-down. We extracted RNAs from the pull-down sample, prepared the strand-specific RNA-Seq libraries and submitted them for deep-sequencing.

2017-07-01 | GSE98218 | GEO

RBPMS mediates smooth muscle specific alternative splicing via oligomerization and modulation of trans splicing factor recruitment

Project description:RBPMS regulates alternative splicing decision via recruiting other trans factors. This experiment aims to investigate the interactome of Strep-II tagged recombinant RBPMS in Hela nuclear extract. The interactome of the full length protein is compared to the construct lacking the far C-terminal 20 amino acids. The “R” series indicates full-length RBPMS pull-down. The “P” series indicates truncated RBPMS pull-down. The “BL” series indicates full length RBPMS pull-down in the absence of nuclear extract input but with bovine serum albumin beads blocking reagent. The “N” series indicates non-baited negative control pull-down.

2023-10-24 | PXD037620 | Pride

RNA-biotin based pull down assay with polyA site (PAS) RNA substrates in Hela Nuclear Extract followed by RNA-seq to discover trans-acting RNA molecules involved in mRNA 3 processing

Project description:We aimed to discover trans-acting RNA molecules involved in mRNA 3 processing. We reasoned that, if there exist such functional RNAs, they must directly associate with the key machinery responsible for mRNA 3 processing. Therefore, it would be of great value to comprehensively identify RNAs interacting with pre-mRNA 3 processing complex. To this goal, we took advantage of previously well-characterized system combined with high-throughput sequencing to investigate the target RNAs at the transcriptomic level. Briefly, we used two polyA site (PAS) RNA substrates, SV40 late (SVL) and adenovirus L3 pre-mRNAs, and corresponding control RNAs with point mutation (U to C) at the highly conserved cis-element AAUAAA. RNA substrates were first biotinylated at the 3 end, and then bound to the streptavidin magnetic beads. After incubation with Hela Nuclear Extract (NE) under polyadenylation condition, the two wild type RNA substrates could specifically recruit mRNA 3 processing factors in NE for complex assembly. The purification of the protein complex and its interacting RNAs were performed using biotin-streptavidin pull-down. we extracted RNAs from the pull-down sample, prepared the strand-specific RNA-Seq libraries and submitted them for deep-sequencing. See related experiments: E-MTAB-5384; E-MTAB-5389

2017-06-01 | E-MTAB-5383 | biostudies-arrayexpress

Identification of human proteins whose binding to the N6-methyladenosine-containing hairpin from 28S rRNA is modulated by methylation

Project description:We have recently found that the human methyltransferase ZCCHC4 is responsible for introducing the single m6A modification in 28S rRNA. The project is aimed at further elucidating the functional consequences of such methylation. To this end, protein mass spectrometry is utilized to identify proteins that bind preferentially to the methylated or unmethylated form of the m6A containing hairpin sequence in 28S rRNA. Specifically, this is done by incubating a HeLa cell extract with an methylated or unmethylated RNA oligonucleotide containing a biotin affinity tag, which is used to pull-down the RNA with associated proteins.

2019-11-22 | PXD013354 | Pride

Examining the stability of nucleosomal modifications during pull-down affinity purification

Project description:Here we investigated the stability of nucleosomal modifications during pull-down affinity purification with HeLa nuclear extracts. Unmodified di-nucleosomes and di-nucleosomes decorated with H3K4me3K9acK14acK18acK23acK27ac, H4K5acK8acK12acK16acK20me2 and incorporating histone variant H2A.Z were incubated with HeLa nuclear extract or buffer alone for 4 hours at 4 degrees Celsius. The relative abundances of nucleosomal modifications were quantified using LC-MS.

2023-12-10 | PXD042823 | Pride

RBPMS mediates smooth muscle specific alternative splicing via oligomerization and modulation of trans factor recruitment

Project description:RBPMS regulate splicing decisions by modulating the transcript-bound proteome. This experiment aims to investigate the proteome assembled on an experimental RNA, TM3 transcript, in human Hela nuclear extract under the various conditions, ± ATP and ± RBPMS. The model RNA is tethered on amylose bead via a protein, MPB-MS2. After pull-down, the protein-RNA complexes are eluted from the beads with maltose. The sample series "N" and "NA" are two negative control conditions. "B" and "R" are sample series of two experimental conditions.

2023-10-24 | PXD037617 | Pride

Biotin pull-down assay of microRNA-25-3p-specific mRNA targets in human hepatic stellate cells

Project description:Biotin pull-down assay of microRNA-25-3p-specific mRNA targets in human hepatic stellate cells

| PRJNA488051 | ENA

RNA pull down assay of GST-ZFP36L1 (wildtype and mutant)

Project description:RNA pull down assay of GST-ZFP36L1 (wildtype and mutant)

| PRJNA561512 | ENA

Identification the proteins interacted with ILF2 in human keratinocytes

Project description:By profiling lncRNA expression changes during human skin wound healing and screening lncRNA functions, we identified SNHG26 as a pivotal regulator in keratinocyte progenitors underpinning this phase transition. we performed RNA pull-down assay in human keratinocyte progenitors and found SNHG26 interact with ILF2. ILF2, or the nuclear condensates it forms, is crucial for maintaining the stability of SNHG26. To identify other protein components within these condensates, we employed a proximity-dependent biotin identification (BioID) assay, which label proteins in close proximity to ILF2 that fused to BioID2, and subsequently identifying them through mass spectrometry (MS).

2024-08-28 | PXD055235 | 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