Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CLIP-Seq of ZCCHC14 binding sites in HAV infected cells

ABSTRACT: We analyzed RNAs bound to FLAG tagged ZCCHC14 protein in HAV infected 293T cells using enhanced crosslinking-immunoprecipitation (eCLIP) and next generation sequencing (NGS), in order to identify ZCCHC14 binding sites on cellular and HAV RNAs.

ORGANISM(S): Homo sapiens

PROVIDER: GSE192599 | GEO | 2022/06/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Mapping cell structure across scales by fusing protein images and interactions

Project description:Enhanced crosslinking and immunoprecipitation assay (eCLIP) for C-terminally FLAG-HA-tagged RPS3A in HEK293T cells.

2021-08-23 | GSE171553 | GEO

Genes regulated by Hfq (PAR-CLIP)

Project description:RNAs that cross-link to proteins were isolated and sequenced from FLAG-tagged Hfq or wild-type strains

2022-10-04 | GSE214592 | GEO

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

HNRPA2B1 HITS-CLIP

Project description:Expression, crosslinking and immunoprecipitation of tagged HNRPA2B1 (variant A2) to identify bound RNA sequences

2012-02-28 | GSE35799 | GEO

GNPS - PAP-gamma associates with PAXT nuclear exosome to control the stability of PROMPT ncRNAs

Project description:Endogenous ZFC3H1 was tagged in 293T cells. Dignam cellular extracts where subjected to sequential FLAG and HA immunoprecipitation and elution. Complexes were then analyzed using mass spectrometry at the taplin mass spectrometry facility. The 2 samples are FLA-HA IP in wild-type 293T cells and Flag-HA IP in FH-ZFC3H1 293T cells.

2022-05-16 | MSV000089482 | GNPS

ENO1's RNA-binding sites in Human HeLa cells using eCLIP

Project description:eCLIP was performed for ENO1 in HeLa cells, following the protocol described by Van Nostrand et al. (2016). Libraries for six immunoprecipitation and size-matched input controls were produced. In addition, libraries were produced for two no-crosslinking controls. The libraries were sequenced using paired-end sequencing (PE125) on an Illumina HiSeq2000 platform.

2020-10-27 | E-MTAB-9031 | biostudies-arrayexpress

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [array]

Project description:RNA binding proteins (RBPs) play essential roles in cellular physiology by interacting with target RNAs. As defects in protein-RNA recognition lead to human disease, UV-crosslinking and immunoprecipitation (CLIP) of ribonuclear complexes followed by deep sequencing (-seq) is critical in constructing protein-RNA maps to expand our understanding of RBP function. However, current CLIP protocols are technically demanding and involve low complexity libraries that yield squandered sequencing of PCR duplicates and high experimental failure rates. To enable truly large-scale implementation of CLIP-seq, we have developed an enhanced CLIP methodology (eCLIP) that features a decrease of ~10 cycles of requisite amplification with a concomitant >60% decrease in discarded PCR duplicate reads, while maintaining the ability to identify RNA binding with single-nucleotide resolution. By simplifying the generation of paired IgG and size-matched input controls, eCLIP also dramatically improves specificity in discovery of authentic binding sites. To demonstrate that eCLIP enables large-scale and robust profiling of RBPs, 102 eCLIP experiments in biological duplicate for a diverse collection of 74 RBPs in HepG2 and K562 cells were completed (available at https://www.encodeproject.org). We establish that eCLIP is comparable in amplification and sample requirements to ChIP-seq, and enables integrative analysis of diverse RBPs to reveal factor-specific profiles, common artifacts for CLIP experiments and RNA-centric perspectives of RBP activity.

2016-03-28 | GSE77339 | GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [iCLIP]

2016-03-28 | GSE77633 | GEO

Enhanced CLIP (eCLIP) enables robust and scalable transcriptome-wide discovery and characterization of RNA binding protein binding sites [eCLIP - 293T cells]

2016-03-28 | GSE77629 | GEO

HNRPA2B1 HITS-CLIP

Project description:Expression, crosslinking and immunoprecipitation of tagged HNRPA2B1 (variant A2) to identify bound RNA sequences RNA molecules that are immunoprecipitated are sequenced followed purification under denaturing conditions

2012-02-28 | E-GEOD-35799 | biostudies-arrayexpress

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