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 the RNA-binding protein (RBP) RBM4 in KBM-7 derived near-haploid human cell line, HAP1.

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE147895 | GEO | 2020/09/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

PAR-CLIP of RBM4 and HIF-2a

Project description:To identify which mRNAs bind to RBM4/HIF-2a Two PAR-CLIPs were performed: One of an RBM4 immunoprecipitation, and the other of a HIF-2a immunoprecipitation and excising the associated RBM4 band.

2012-05-06 | E-GEOD-36247 | biostudies-arrayexpress

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: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.

| PRJNA622499 | ENA

RNA-sequencing experiments to identify differentially expressed genes between Wild Type and RBM4 KO HAP1 cell line samples

Project description:Here, we implemented a computational pipeline to determine the correlation of expression between individual RBPs and ERVs from single-cell or bulk RNA sequencing data. One of our top candidates for an RBP negatively regulating ERV expression was RNA-Binding Motif Protein 4 (RBM4). This set of bulk RNA-sequencing experiments was performed to identify differentially expressed genes and repetitive elements, particularly HERVs, between independent Wild Type and RBM4 KO clones in the KBM-7 derived, near-haploid human cell line, HAP1

2020-09-03 | GSE147893 | GEO

RBM4 regulates senescence

Project description:RNA-seq was performed on A549 and H1299 cells that stably knocking down RBM4 or control, in order to profile the gene expression change that were regulated by RBM4

2023-02-01 | GSE111051 | GEO

Effect of depletion of RBM4 on gene expression of esophageal squamous cell carcinoma cell KYSE150

Project description:To explore the role of RBM4 in esophageal squamous cell carcinoma cell,we performed high-throughput mRNA sequencing (mRNA-seq) in KYSE150 with stable knockdown of RBM4 by shRNA . We then performed gene expression profiling analysis using data obtained from RNA-seq of KYSE150 cells,three replicates were sequenced.

2023-04-26 | GSE220613 | GEO

Cold induced RNA-binding proteins influence alternative polyadenylation

Project description:We employed PAR-CLIP, a recently developed method based on RNA-protein crosslinking, to identify Cirbp and Rbm3 binding sites at transcriptome-level. Genome-wide RNA-seq analysis indicated that cold temperature leads to extensive 3M-bM-^@M-^YUTR lengthening whereas the loss of Cirbp or Rbm3 resulted in 3M-bM-^@M-^YUTR shortening. Combining with PAR-CLIP results, we found that these two RBPs repress the polyadenylation adjacent to their binding sites. Examination of the binding sites of Cirbp and Rbm3 by PAR-CLIP and their influence on the transcriptome by RNA-seq. PARCLIP was performed as in Hafner et al. 2010 Cell 141, 129M-bM-^@M-^S141, with MEFs cell lines stably expressing FLAG-tagged Cirbp and Rbm3. We used 4-thiouridine (4SU) to enhance the crosslink. For RNA-seq, polyadenylated RNA from the mock-transfected cells at 37M-BM-0C or 32M-BM-0C with two replicates, siCirbp-1, siCirbp-2, siRbm3-1 and siRbm3-2 MEFs at 37M-BM-0C were sequenced on Solexa GAII using 76bp single-end kits according to the manufacturerM-bM-^@M-^Ys instructions.

2013-05-01 | E-GEOD-40468 | biostudies-arrayexpress

Homo sapiens

Project description:PAR-CLIP of RBM4 and HIF-2a

| PRJNA153059 | ENA

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins (CLIP)

Project description:Crosslinking and immunoprecipitation (CLIP) is increasingly used to map transcriptome-wide binding sites of RNA-binding proteins (RBPs). We developed a method for CLIP data analysis and applied it to compare 254 nm CLIP with PAR-CLIP, which involves crosslinking of photoreactive nucleotides with 365 nm UV light. We found small differences in the accuracy of these methods in identifying binding sites of HuR, a protein that binds low-complexity sequences and Argonaute 2, which has a complex binding specificity. We show that crosslink-induced mutations lead to single-nucleotide resolution for both PAR-CLIP and CLIP. Our results confirm the expectation from original CLIP publications that RNA-binding proteins do not protect sufficiently their sites under the denaturing conditions used during the CLIP procedure, and we show that extensive digestion with sequence-specific ribonucleases strongly biases the set of recovered binding sites. We finally show that this bias can be substantially reduced by milder nuclease digestion conditions. We performed duplicate experiments for each variant of the CLIP protocol (CLIP, PAR-CLIP), each protein (HuR, Ago2), and enzymatic digestion (complete T1 digestion, mild MNase digestion). In addition, we performed a single PAR-CLIP experiment with mild T1 digestion.

2011-05-15 | E-GEOD-28859 | biostudies-arrayexpress

mRNA regions where 80S ribosomes pause during translation elongation in vivo interact with protein uS19, a component of the decoding site

Project description:80S-ribosome bound uS19 translatome-wide crosslinking sites in human mRNAs revealed by PAR-CLIP

2019-03-14 | GSE128265 | GEO

RBM4 regulates senescence

Project description:RBM4 regulates senescence

| PRJNA435720 | ENA