Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Effect of the depletion of RBP33 (Tb927.8.990) on the transcriptome of bloodstream and procyclic Trypanosome brucei [RNA-seq]

ABSTRACT: RBP33 depletion results in the overexpression of 40% (bloodstream) or 20% (procyclic) of all transcripts annotated in the 427 2018 genome

ORGANISM(S): Trypanosoma brucei brucei

PROVIDER: GSE186563 | GEO | 2022/11/03

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Surface Proteome Analysis of Procyclic and Bloodstream forms of Trypanosoma brucei

Project description:Surface-exposed proteins of the bloodstream and procyclic forms of T. brucei were biotinylated, affinity purified using streptavidin, and analyzed by LC-MS/MS

2015-03-17 | MSV000079080 | MassIVE

Effect of the depletion of ZC3H41 (Tb927.11.1980) on the transcriptome of procyclic Trypanosome brucei

Project description:Depletion of ZC3H41 has minor effects on the transcriptome of procyclic trypanosomes. In general, ZC3H41-regulated transcripts seem to be expressed at low abundance, and almost half of them (43%) are probably non-coding, since the corresponding encoded proteins have not been detected in proteomic surveys . A transcript encoding a trans-sialidase (Tb927.11.11410) was clearly upregulated in ZC3H41-depleted cells .

2023-03-29 | GSE212921 | GEO

Transcription profiling of Trypanosoma brucei BSF and PCF monomorphic cells

Project description:Cy3 and Cy5 direct labelled RNA from Bloodstream MiTat1.1 trypanosomes and Procyclic 427 Lister were hybridized onto JCVI Trypanosoma brucei oligoarrays (version2). Procyclic RNA were used as control for data analysis.

2010-01-01 | E-MEXP-2028 | biostudies-arrayexpress

Oxford Nanopore sequencing of poly(A)+ RNA from two Trypanosoma brucei strains

Project description:EATRO1125 bloodstream forms grown to about 5 x 10e5 per ml. Lister 427 procyclic forms at no more than 2 million per ml. Direct nanopore sequencing on cells approaching their expiration date.

2020-07-16 | E-MTAB-9319 | biostudies-arrayexpress

Transcription profiling of T. brucei bloodstream and procyclic forms to look at differential expression of membrane-trafficking genes

Project description:To look at differential expression of membrane-trafficking genes, <br>we extracted RNA from exponentially growing cultures of T. brucei <br>bloodstream (BSF) and procyclic (PCF) forms, labelled and competitively <br>hybridised the cDNA to the microarray. 8 arrays, representing <br>6 BSF and 5 PCF biological replicates, as well as dye swaps were used.

2008-06-26 | E-MEXP-1529 | biostudies-arrayexpress

Comparative phosphoproteome of Trypanosoma brucei bloodstream & procyclic form

Project description:Comparative phosphoproteomic analysis of SILAC labelled cultured bloodstream and procyclic form Trypansoma brucei. Phosphopeptide enrichement via SCX and TiO2, acquired on Oribtrap Velos using MSA. Triplicate biological replicate for each lifecycle stage (as unmixed, and two SILAC label swap expreiments), eight fraction injected in technical triplicate. For the SILAC labelled samples, the corresponding changes in the proteome were measured using unenriched peptides sperated by SCX. Data was processed using MaxQuant version 1.3.0.5 which incorporates the Andromeda search engine. Proteins were identified by searching a protein sequence database containingT. brucei brucei 927 annotated proteins (Version 4.0, downloaded from TriTrypDB http://www.tritrypdb.org/ supplemented with the VSG221 sequence and frequently observed contaminants (porcine trypsin, bovine serum albumins and mammalian keratins) that contains a total of 10,081 protein sequences. Search parameters specified an MS tolerance of 6 ppm, an MS/MS tolerance at 0.5 Da and full trypsin specificity, allowing for up to two missed cleavages. Carbamidomethylation of cysteine was set as a fixed modification and oxidation of methionines, N-terminal protein acetylation and N-pyroglutamate were allowed as variable modifications. Phosphoproteomic analysis included phosophorylation of serine, threonine and tyrosine as additional variable modifications. Peptides were required to be at least 7 amino acids in length and a MaxQuant score >5, with false discovery rates (FDRs) of 0.01 calculated at the levels of peptides, proteins and modification sites based on the number of hits against the reversed sequence database.

2013-07-03 | PXD000049 | Pride

Time series RNA-seq of temperature-entrained and light-entrained bloodstream and procyclic form Trypanosoma brucei cultures

Project description:To address whether T. brucei has a circadian clock we probed its transcriptome by RNA-seq, searching for transcripts oscillating with a 24 hr period. For this we entrained/ synchronized parasites in vitro for three days using temperature and light as environmental stimuli and then collected parasite RNA every four hours for two consecutive days. Parasite RNA was subjected to RNA-seq analysis. We performed this protocol on two stages of the T. brucei life cycle (bloodstream and insect procyclic forms).

2017-02-10 | E-MTAB-4952 | biostudies-arrayexpress

Widespread variation in transcript abundance within and across developmental stages of Trypanosoma brucei

Project description:Whole genome comparison of RNA levels for both protein coding genes and structural RNAs in five different life cycle stages: in vivo slender bloodstream form, in vivo stumpy bloodstream form, cultured bloodstream form, log-phase procyclic culture form and stationary-phase procyclic culture form

2009-09-24 | GSE18049 | GEO

Identification of CARP3-interacting proteins in Trypanosoma brucei bloodstream forms and procyclic forms

Project description:How flagellar signaling regulates the host interaction of parasites remains a challenge due to poor conservation of signaling systems with those in cilia of higher organisms. The trypanosome-specific cAMP response protein 3 (CARP3) shows developmentally regulated localization at the flagellar tip membrane, where it is essential for parasite swarming and colonization of the tsetse fly insect vector. This project describes identification of CARP3-YFP interacting proteins by GFP trap pull down followed by mass spectrometry in the bloodstream stage as well as in the procyclic stage of Trypanosoma brucei.

2022-08-31 | PXD025398 | Pride

Transcription profiling of procyclic Trypanosoma brucei cultured at 27oC or under heat shock stress conditions at 41oC

Project description:Procyclic trypanosomes (strain 427 lister) were grown in culture under standard conditions at 27ºC in SDM79 medium with 10% foetal bovine serume (Brun and Schnenberger, 1979), in a gazed incubator (5% CO2). Logarithmically growing procyclic cells (at about 5*10^6 cells/ml, at 27°C) were added to one volume medium that had been heated to 53°C and incubated at 41ºC for 60 minutes in a waterbath in a closed tube (41ºC sample). The control cells were added to one volume medium at 27ºC and also incubated for 60 minutes in a closed tube at 27°C. Cells were harvested and washed once in PBS. The harvesting was done within 8 minutes.

2008-09-10 | E-MEXP-1476 | 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