Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of RNA-binding proteins (RBPs), LIN28A, LIN28B Igf2bp3 and Pum2 in 220-8 mouse cell lines

ABSTRACT: Transcriptome-wide profiling of RNA-binding by four RBPs in v-Abl transformed 220-8 pro-B mouse cell line. Binding sites are characterized by T-to-C cross-linking mutations, depth, location on transcript, and overlap/exclusivity across different RBPs.

ORGANISM(S): Mus musculus

PROVIDER: GSE98465 | GEO | 2019/06/27

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of RNA-binding proteins (RBPs), IGF2BP1 and IGF2BP3 in the K562 CML-derived cell line

Project description:Transcriptome-wide profiling of RNA-binding by IGF2BP1 and IGF2BP3 in the K562 cell line. Binding sites are characterized by T-to-C cross-linking mutations, depth and location on transcript

2020-02-10 | GSE138063 | GEO

Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of RNA-binding proteins (RBPs), IGF2BP1 and IGF2BP3 in the K562 CML-derived cell line

Project description:Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of RNA-binding proteins (RBPs), IGF2BP1 and IGF2BP3 in the K562 CML-derived cell line

| PRJNA574408 | ENA

Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3.

Project description: Not available

| S-EPMC6672051 | biostudies-literature

LIN28B, LIN28A, KISS1, and KISS1R in idiopathic central precocious puberty.

Project description: Not available

| S-EPMC3184284 | biostudies-literature

Lin28A and Lin28B inhibit let-7 microRNA biogenesis by distinct mechanisms.

Project description: Not available

| S-EPMC3227872 | biostudies-literature

Optimized Infra-red photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (IR-PAR-CLIP) protocol identifies novel IGF2BP3-interacting RNAs in colon cancer cells

Project description:We report the PAR-CLIP data for endogenous IGF2BP3 protein in colorectal carcinoma cell line (HCT116). In this study, we established an immunoprecipitation protocol to obtain highly pure endogenous IGF2BP3-RNA complexes and compared RNase cleavage conditions. The PAR-CLIP protocol was modified to use single adapter circular ligation approach to increase the efficiency in library preparation and reduce sequence bias. Moreover, we implemented the use of highly-sensitive infra-red (IR) fluorescent dyes instead of radioactive probes to visualize IGF2BP3-crosslinked RNAs. We named the modified method “IR-PAR-CLIP”.

2023-08-17 | GSE229653 | GEO

RNA-affinity isolations 13 RBPs

Project description:To identify RNAs specifically associated with potential RBPs, yeast cells expressing TAP-tagged RBP or the wild-type strain BY4741 (mock control) were grown to mid-log phase in rich medium and harvested by centrifugation. RNA affinity isolations were essentially performed as described (Gerber et al. 2004 PLoS Biol.; see protocol). In brief, TAP-tagged protein were captured from cell extracts with IgG coupled agarose beads (Sigma) and released by incubation with a site-specific protease (AcTEV, Sigma). from the extract (input) and from the affinity isolates was purified with the RNeasy Mini/ Micro Kit (Qiagen). RNAs were reverse transcribed using a mixture of oligo-dT and random nonamer oligos in the presence of amino-allyl dUTP/dNTP mixture. cDNAs were fluorescently labeled and hybridized on yeast oligo microarrays over night at 42 degrees in formamide-based hybridization buffer. Antigenic peptide used in IP: TAP-tag An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

2010-12-06 | E-GEOD-21864 | biostudies-arrayexpress

CRISPR/Cas9 screening of RNA binding proteins (RBPs) that regulate RUNX1 isoform production

Project description:The proper balance of hematopoietic stem cell (HSC) self-renewal and differentiation is critical for normal hematopoiesis and disrupted in hematologic malignancy. Among regulators of HSC fate, transcription factors have a well-defined, central role and mutations promote malignant transformation. More recently, studies have illuminated the importance of post-transcriptional regulation by RNA-binding proteins (RBPs) in hematopoiesis and leukemia development. However, the RBPs involved and breadth of regulation are only beginning to be elucidated. Furthermore, the intersection between post-transcriptional regulation and hematopoietic transcription factor function is poorly understood. Here, we studied the post-transcriptional regulation of RUNX1, a key hematopoietic transcription factor. Alternative polyadenylation (APA) of RUNX1 produces functionally antagonistic protein isoforms (RUNX1a versus RUNX1b/c) that mediate HSC self-renewal versus differentiation, an RNA-processing event that is dysregulated in malignancy. Consequently, RBPs that regulate this event directly contribute to healthy and aberrant hematopoiesis. We modeled RUNX1 APA using a split GFP minigene reporter and confirmed the sensitivity of our model to detecting changes in RNA-processing. We utilized this reporter in a CRISPR screen consisting of single guide-RNAs exclusively targeting RBPs and uncovered HNRNPA1 and KHDRBS1 as antagonistic regulators of RUNX1a isoform generation. Overall, our study provides mechanistic insight into the post-transcriptional regulation of a key hematopoietic transcription factor and identifies RBPs which may have a widespread, important function in hematopoiesis.

2021-03-16 | GSE145968 | GEO

Prognostic value of Lin28A and Lin28B in various human malignancies: a systematic review and meta-analysis.

Project description: Not available

| S-EPMC6444518 | biostudies-literature

Photoactivatable-Ribonucleotide-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) of the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.

Project description:We hypothesized that RBM4 regulates HERVs by directly binding to their transcripts. To test this possibility, we performed photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation (PAR-CLIP). We performed four independent PAR-CLIP replicates of our own using HAP1 cells stably expressing a FLAG-tagged RBM4 (FLAG-RBM4) transgene under control of a doxycycline-inducible promoter. Following metabolic labeling with 4-thiouridine (4SU) and crosslinking with ultraviolet light (UV) of 312 nm wavelength, we isolated RNA covalently linked to FLAG-RBM4. The RNA recovered from four biological replicates was converted into cDNA libraries and deep sequenced.

2020-09-03 | GSE147895 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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