Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CPSF-160 iCLIP

ABSTRACT: We performed iCLIP of CPSF-160- GFP as CPSF160 was believed to be the main RNA-binding subunit of CPSF. To this end, we used a stable HeLa cell line that expresses GFP-CPSF160 in a doxycycline (Dox)-dependent manner. After GFP-CPSF160 was induced, we irradiated the cells with UV-C (wavelength=254nm) to induce protein-RNA crosslinks and immunoprecipitated the complex with a GFP antibody.

INSTRUMENT(S): iCLIP materials, Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Ina Huppertz

PROVIDER: E-MTAB-2939 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Project description:UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are the most frequently used methods to study protein-RNA interactions in the intact cells and tissues, but their relative advantages or inherent biases have not been evaluated. To benchmark CLIP and iCLIP method, we performed iCLIP with Nova protein, which is the most extensively studied protein by CLIP. Further, we assessed UV-C-induced cross-linking preferences, by exploiting the UV-independent formation of covalent RNA cross-links of the mutant RNA methylase NSUN2.

2012-07-20 | E-MTAB-1008 | biostudies-arrayexpress

hiCLIP analysis of RNA duplexes bound by STAU1 in HEK293 cells

Project description:hiCLIP protocol was followed to isolate RNA bound to 3XFLAG-STAU1 protein and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction, and are specified below for each sequencing run. Random barcodes were also incoperated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina paired-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

2015-03-02 | E-MTAB-2937 | biostudies-arrayexpress

Analysis of ribosomal occupancy with ribosome profiling.

Project description:Ribosome profiling was prepared in parallel with RNA-seq, using the same protocol for cDNA library preparation.

2015-03-01 | E-MTAB-2941 | biostudies-arrayexpress

Expression profiling by high throughput sequencing

Project description:RNAseq was prepared in parallel with ribosome profiling, using the same protocol for cDNA library preparation.

2015-03-01 | E-MTAB-2940 | biostudies-arrayexpress

iCLIP analysis of RNA bound by FUS in human brain

Project description:RNA abundance decreases linearly from the 5′ to 3′ end of long introns to create “saw-tooth” patterns, and these can be used to infer locations of major splicing events. FUS binds across entire pre-mRNAs with limited sequence specificity, permitting examination of these saw-tooth patterns. We used FUS iCLIP from the human brain to identify deviations from the expected linear decrease of reads across long introns that correspond to recursive splicing events. iCLIP protocol was followed to isolate RNA bound to FUS protein and amplify cDNA library as described in the manuscript. Specific barcodes were used for each RT reaction, and are specified in the library construction protocol for each sequencing run. Random barcodes were also incorporated into cDNAs to distinguish between PCR duplication of cDNA products. The final products were obtained by PCR with Illumina paired-end sequencing primers: 5-CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT-3; 5-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3

2015-05-05 | E-MTAB-3534 | biostudies-arrayexpress

CLIP-Seq of human brain and neuroblastoma sample to characterisethe RNA targets and position-dependent splicing regulation by TDP-43

Project description:iCLIP (UV-crosslinking and immunoprecipitation followed by sequencing ) analysis of TDP-43 RNA binding sites

2011-07-21 | E-MTAB-530 | biostudies-arrayexpress

PRPF8 iCLIP on HeLa cells in response to eIF4A3 Knockdown

Project description:This experiment uses iCLIP to identify the binding pattern of the spliceosomal protein PRPF8 on RNA. The data shows that PRPF8 binds strongly and specifically in the region 12 to 14nt upstream of 5' splice sites (5ss). Due to PRPF8's role in the formation of the catalytically active spliceosome, this data can be used as a readout of 5ss selection. Here, we performed iCLIP on HeLa cells treated with control or EIF4A3 siRNA, with 4 replicate samples per condition and eIF4A3 protein levels reduced ~50% in knockdown. We investigated the role of the exon junction complex (EJC) in suppressing 5ss that are reconstituted at the junction of two canonical exons (RS-5ss) - selection of these splice sites would result in recursive splicing of canonical exons. We plotted the crosslink sites of reads that span an exon-exon junction, seperating reads that span RS-5ss from those that do not. We found that reads that span an RS-5ss are enriched at the 12-14nt window associated with 5ss selection, while reads that span other exon-exon junctions are not enriched. This effect is magnified greatly by knockdown of eIF4A3. The results indicate that RS-5ss can be used by the spliceosome, but that this process is usually repressed by the EJC. This data is evidence of recursive splicing of canonical exons and the role of the EJC in repressing recursive splicing.

2018-10-14 | E-MTAB-7269 | biostudies-arrayexpress

SERBP1 iCLIP in mitotic and asynchronous cells with Blu577 treatment

Project description:In the associated paper, SERBP1 is shown to form granules in mitotic cells in a PKCɛ-dependent manner (M-bodies). We performed SERBP1 iCLIP in DLD1 cells that were either asynchronous or enriched for mitotic cells and after treatment with 2 hours of 500nM Blu577 or equivalent DMSO. We found that SERBP1 alters its positioning on rRNA in mitosis in a Blu577-dependent manner, identifying an alternative binding position that coincides with the formation of M-bodies. Mitotic enrichment was performed by single thymidine block, release in to G2 block with RO3306, and release and mitotic shake-off. The fastq files provided are demultiplexed, with adapters and barcodes trimmed and UMI sequences are found in the fastq headers.

2021-10-05 | E-MTAB-10830 | biostudies-arrayexpress

Spliceosome iCLIP

Project description:The studies of spliceosomal interactions are challenging due to their dynamic nature. Here we developed spliceosome iCLIP, which immunoprecipitates SmB along with snRNPs and auxiliary RNA binding proteins (RBPs) to simultaneously map the spliceosomal binding to human snRNAs and pre-mRNAs. This identified 9 distinct regions on pre-mRNAs, which overlap with position-dependent binding patterns of 15 RBPs. Using spliceosome iCLIP, we additionally identified >50,000 branchpoints (BPs) that have canonical features, unlike those identified by RNA-seq. The iCLIP BPs generally overlap with the computationally predicted BPs, and alternative BPs are associated with extended regions of structurally accessible RNA. We find that the position and strength of BPs defines the binding patterns of SF3 and U2AF complexes, whereas the RNA structure around BPs affects the sensitivity of exons to perturbation of these complexes. Our findings introduce spliceosome iCLIP as a new method for transcriptomic studies of BPs and splicing mechanisms.

2019-08-30 | E-MTAB-6950 | biostudies-arrayexpress

Spliceosome iCLIP in multiple cell lines

2019-08-03 | E-MTAB-8182 | biostudies-arrayexpress

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