Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of proteins associated with KhpA and khpB in the bacterium Deinococcus radiodurans

ABSTRACT: To examine if this is also the case in D. radiodurans and what other proteins interact with KhpA/KhpB proteins in D. radiodurans, KhpA and KhpB were tagged with 3FLAG epitope at the C-terminus chromosomally or through expression on the pRADgro plasmid, followed by protein-protein coimmunoprecipitation (coIP) experiments. Compared to WT, only 8 proteins were enriched significantly with KhpA-3FLAG relative to the WT strain expressing untagged KhpA on pRADgro. By contrast, 28 proteins were significantly enriched with KhpB-3xFLAG.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Deinococcus Radiodurans R1 (ncbitaxon:243230)

SUBMITTER: Lydia M. Contreras

PROVIDER: MSV000094865 | MassIVE | Fri May 24 09:03:00 BST 2024

SECONDARY ACCESSION(S): PXD052557

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of RNA molecules associated with the RNA-chaperone Hfq

Project description:We used high-throughput methods to discover the Salmonella RNAs that are targeted by the bacterial Sm-like protein, Hfq. Our generic approach, using chromosomal epitope tagging and coIP-on-chip will also be useful to identify the post-transcriptional regulons of many other RNA-binding proteins. Keywords: coIP-chip To identify the direct Hfq RNA targets, we co-immunoprecipitated RNA from a strain expressing a 3xFLAG-tagged Hfq-protein using an anti-3xFLAG antibody. As a negative control, we used the same antibody (anti-3xFLAG) to co-immunoprecipitate RNA from an isogenic strain expressing the non-tagged Hfq-protein. Two independent biological replicates were generated.

2010-06-20 | E-GEOD-10149 | biostudies-arrayexpress

Identification of RNA molecules associated with the RNA-chaperone Hfq

2008-08-23 | GSE10149 | GEO

Chromatin immunoprecipitation of yeast and CoIP-chip of nucleosome-enriched chromatin after immunoprecipitation for specific factors

Project description:ChIP-chip & CoIP-chip of nucleosome enriched chromatin after IP of specific factors

2009-09-25 | E-MEXP-1847 | biostudies-arrayexpress

ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1)

Project description:ChIP-chip to determine the regulation of the K. lactis hsgs (ChIP of MATa1, MATalpha2, and RME1). The MATa1 and MATalpha2 ChIPs were performed in an a/alpha cell using N-terminally HA-tagged proteins and the RME1 ChIPs were perfomed in an a cell using C-terminally myc-tagged protein. For the RME1 ChIPs, the cells grown with out phosphate. For the MATa1 andMATalpha2 ChIPs the cells were grown in YEPD. Epitope tagged strains were compared to untagged control strains. Two biological replicates were preformed for the RME1 ChIP. For the MATa1 and MATalpha2 ChIP, peaks were considered indicative of binding if both MATa1 and MATalpha2 showed enrichment above the untagged control.

2010-12-01 | E-GEOD-25209 | biostudies-arrayexpress

HeLa CD4+ transfection

Project description:Expression profiles of HeLa CD4+ cells transfected with epitope-tagged eTat plasmid, or parental plasmid pCep4. Cells are unsynchronized and untreated. Keywords: other

2003-08-04 | GSE570 | GEO

Two MADS-box transcription factors mediate epigenetic control of tomato fruit ripening [ChIP-seq]

Project description:Using ChIP-seq to study the deposition of RIN in WT tomato AC fruits and pCBC::RIN-3xFLAG, pCBC::RIN-3xFLAG/dml2-3 tagline fruits at 34 dpa (Breaker stage)

2026-05-08 | GSE210588 | GEO

RNF4 interactome in heatshocked HeLa cells

Project description:Exposure of cells to heat or oxidative stress causes misfolding of proteins. To avoid toxic protein aggregation, cells have evolved nuclear and cytosolic protein quality control (PQC) systems. In response to proteotoxic stress cells also limit protein synthesis by triggering transient storage of mRNAs and RNA binding proteins (RBPs) in cytosolic stress granules (SGs). We demonstrate that the SUMO-targeted ubiquitin ligase (StUbL) pathway, which is part of the nuclear proteostasis network, regulates SG dynamics. We provide evidence that inactivation of SUMO deconjugases under proteotoxic stress initiates SUMO-primed, RNF4-dependent ubiquitylation of RBPs that typically condense into SGs. Impairment of SUMO-primed ubiquitylation drastically delays SG resolution upon stress release. Importantly, the StUbL system regulates compartmentalization of an amyotrophic lateral sclerosis (ALS)-associated mutant of FUS in SGs. We propose that the StUbL system functions as surveillance pathway for aggregation-prone RBPs in the nucleus thereby linking the nuclear and cytosolic axis of proteotoxic stress response. To better understand the role of RNF4 in the proteotoxic stress response we aimed to identify RNF4-associated protein complexes in cells exposed to heat stress. To allow immuno-affinity purification of endogenous RNF4 on anti-Flag agarose beads we used CRISPR/Cas9-mediated gene editing to integrate a C-terminal 3xFlag epitope tag into the genomic locus of RNF4 in HeLa cells. For the IP-MS experiment HeLa-RNF4-3xFlag cells or parental untagged control cells were exposed to heat stress for 1 h and RNF4-3xFlag together with associated proteins was captured on anti-Flag affinity beads. Tryptic peptides were analyzed by LC-MS/MS and data from three replicates were quantified by the Max Quant label-free quantification (LFQ) algorithm.

2023-06-30 | PXD017888 | Pride

ChIP-seq of biofilm master regulators in four species of Candida

Project description:The purpose of this experiment was to identify the genes bound by the biofilm master regulators (Bcr1, Brg1, Efg1, Ndt80, Rob1 and Tec2) in Candida albicans, C. dubliniensis, C. tropicalis and C. parapsilosis during biofilm formation. The regulators were tagged with a c-myc epitope and the immunoprecipitation of the tagged strain was compared to that of an untagged control strain.

2021-04-14 | GSE161133 | GEO

ChIP-Seq data of the Streptomyces venezualae protein Sven6563 (RsrR)

Project description:We report the results of ChIP-Seq experiment investigating the Rrf2 family transciptional regulator RsrR (putatively name Redox sensitive response regulator). The experiment utilized an in trans copy of rsrR with an N-terminal 3xFlag tag encoded on the plasmid pMS82 (containing a phiBT1 integration site). The experiment utilized beads associated with anti-flag antibodies, specific for the Flag tagged protein and a WT host strain. We report >600 target binding sites for the RsrR regulon encompassing a broad range of functional targets with specific reference to those associate with NADPH and NADH metabolism and synthesis.

2017-02-12 | GSE81073 | GEO

RNA interactome profiling in hypervirulent Klebsiella pneumoniae

Project description:To map the Hfq-mediated RNA regulatory network in HvKP, we harnessed the LiRIP-seq approach recently established in our lab, which enabled global profiling of RNA-RNA interactomes in live bacteria. Transformation of the pBAD-t4rnl1 plasmid into Klebsiella allowed us to express T4 RNA ligase 1 for proximity-ligation of RNAs in vivo, followed by co-immunoprecipitation (coIP) to enrich the Hfq-bound RNA transcripts (singleton reads) and ligated RNA fragments (chimeras: sRNA-mRNA, sRNA-sRNA, etc).

2024-07-17 | GSE243246 | GEO

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