Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Interacting partners of Trypanosoma brucei RBSR1 and RBSR2

ABSTRACT: Affinity purification of RBSR1 and RBSR2 endogenously tagged with TAP at the C terminal. A cell line with inducible G-TAP was used as negative control. 3 biological replicates were used for RBSR1 and RBSR2 and 3 technical replicates for GFP

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Trypanosoma Brucei

SUBMITTER: Thomas Ruppert

LAB HEAD: Thomas Ruppert

PROVIDER: PXD033509 | Pride | 2022-10-15

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

: Interacting partners of Trypanosoma brucei CPSF73 in the presence of mRNA processing inhibitor, AN7973

Project description:T. brucei CPSF73 endogenously TAP-tagged at the C-terminal was affinity purified after treating the cells for 15 min with AN7973 at 10x EC50. Three technical replicates were used. 3 technical replicates of untreated cells served as controls. Inducible GFP-TAP with and without treatment served as additional controls

2022-10-19 | PXD033513 | Pride

Interacting partners of Trypanosoma brucei EIF4E2

Project description:Affinity purification of EIF4E2 endogenously tagged with PTP. A cell line with inducible GFP-PTP was used as negative control brucei. 3 biological replicates were used for both EIF4E2 and GFP.

2022-10-18 | PXD033511 | Pride

3' isoform specific RNA IP (3' isRIP-seq) for PUF3 RBP in budding yeast

Project description:Exponentially growing cells (OD 0.5-0.8) from the TAP-tagged strain were harvested by ultracentrifugation followed by of washing and flash freezing in liquid nitrogen and breakage in FastPrep24 (ZYmoresearch S6005). The lysate was subjected to IP with Dyna M280 sheep anti rabbit IgG beads for 2h at 4C. An aliquot was taken before the IP as an input control. The IP of the RNA-protein complex was subjected to cleavage by TEV protease to cleave the TAP-tag off the protein. The bound RNA was then precipitated in phenol/chloroform/isoamyl-alcohol and sequenced using 3' T-filling protocol as described by Wilkening et al 2013 to obtain accurate quantification of 3' isoforms. We used the R Bioconductor package DESeq2 (Anders and Huber 2010) to call for differential log change between the Input and the RNA-IP sample and took all those isoforms as differentially regulated which had more than 4-fold change at a FDR of 10% as reported by the package.

2014-11-13 | E-MTAB-2103 | biostudies-arrayexpress

Identification and functional characterization of proteins interacting with cohesin complex in yeast Saccharomyces cerevisiae.

Project description:To ensure equal separation of DNA, sister chromatids are held together from S phase to metaphase–anaphase transition by a multiprotein complex called cohesin. This makes it possible to establish chromosome biorientation, counteracts the pulling force of mitotic spindle microtubules, preventing premature sister chromatid separation, and ensures precise segregation of sister DNAs into daughter cells In order to better understand how the sister chromatid cohesion process is regulated we looked for new cohesin interacors. We constructed a yeast strain endogenously expressing TAP-tagged Scc1 (Scc1-TAP). Next, we performed a single-step TAP purification using an untagged strain (mock sample) or a strain expressing Scc1-TAP, followed by identification of co-purifying proteins by MS.

2023-10-24 | PXD037034 | Pride

Microarray analysis of TAP::ALG-1 associated RNAs isolated from synchronized 'wild-type' animals and 'mir-58' mutants

Project description:To discover new miRNA targets, we generated a C. elegans transgenic line expressing a functional N-terminally Tandem Affinity Purification (TAP) tagged ALG-1 protein (C. elegans strain WS4303). We crossed the TAP::ALG-1 transgene into the mir-58(n4640) mutant background to generate the strain WS5041. For simplicity, we will hereafter term the TAP::ALG-1 transgenic animals as wild typeand the transgenic WS5041 animals as mir-58. We compared the mRNA population that coimmunopurified with TAP::ALG-1 from synchronized L4 stage wild-type animals with that from synchronized L4 stage mir-58 mutant animals by one-color Affymetrix gene arrays. miR-58 target mRNAs should be specifically underrepresented in the latter samples. Strains WS4303 (wt) and WS5041 (mir-58) were used for TAP::ALG-1 IPs. All experiments were conducted in three independent replicates. For each replicate, WS4303 and WS5041 were grown in parallel. 150 ng of TAP::ALG-1 associated RNA isolated from synchronized late L4 animals were sent to the GeneCore facilty in Heidelberg, Germany (http://www.genecore.embl.de/index.cfm), and the microarray data were generated according to their standard protocol (Weinmann et al. 2009).

2012-03-01 | E-GEOD-32942 | biostudies-arrayexpress

RNAseq of ZC3H5 interacting mRNA

Project description:Bloodstream-form trypanosomes (Lister 427) constitutively expressing ZC3H5-TAP (Tb927.3.740) were used. The protein was pulled down with an IgG column , then the protein and bound RNA was eluted using TEV protease. RNA was then sequenced from unbound (flow-through) and bound (eluate) fractions.

2020-06-06 | E-MTAB-9084 | biostudies-arrayexpress

Mass Spectrometry of NOT gene-related purifications

Project description:Mass Spectrometry of NOT gene-related purifications, including NOT5 Tap Tag in WT and not4 deletion, the Ribosome Nascent Chain Complex, and aggregates in NOT5 Delta,

2022-07-26 | PXD021580 | Pride

Transcription profiling of S. cerevisiae to identify Upf1p-associated transcripts in S. cerevisiae

Project description:The goal of this experiment was to identify transcripts associated with the S. cerevisiae Upf1 protein. Experiment Overall Design: The RNA population from four independent pairs of Upf1p-TAP and mock affinity selections were analyzed by using Affymetrix Yeast Genome S98 Arrays.

2008-06-16 | E-GEOD-9486 | biostudies-arrayexpress

Shg1p associated RNAs

Project description:RNA co-immunopurification with TAP-tagged Shg1p (a component of the Set1 histone methyltransferase complex, SET1C) from Saccharomyces cerevisiae. An untagged (BY4741) served as a control (Gerber et al. 2004). Cells were grown to mid-log phase in rich media and harvested by centrifugation. TAP-tagged Shg1 was affinity-purified from cell-free extracts with IgG sepharose and eluted with TEV protease. RNA was isolated from extract (=input) and from the purified protein sample with the RNAeasy 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. For the method see experimental procedure for RNA IP (Gerber/Dichtl). An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract.

2010-06-24 | E-GEOD-15247 | biostudies-arrayexpress

R2TP_TAP-MS - R2TP/Prefoldin-like component RUVBL1/RUVBL2 directly interacts with ZNHIT2 to regulate assembly of U5 small nuclear ribonucleoprotein

Project description:The R2TP/Prefoldin-like (R2TP/PFDL) complex is a cochaperone complex involved in the assembly of a number of critical protein complexes. Here we use multiple target tandem affinity purification (TAP) coupled to mass spectrometry to map out the interaction network around R2TP/PFDL.

2018-10-24 | PXD006198 | Pride

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