Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomes from Trypanosoma brucei brucei EATRO1125 before and after differentiation of bloodstream forms to procyclic forms

ABSTRACT: Most protozoan pathogens of mammals are transmitted by invertebrate vectors and a comparison of transcriptomes of the developmental forms provides information on genes involved in interactions with different hosts. Trypanosoma brucei is the causal agent of African Trypanosomiasis and is transmitted by Tsetse flies. Here, cultured mammalian bloodstream forms were differentiated in vitro to insect procyclic forms and RNAseq experiments performed on the two developmental forms.

INSTRUMENT(S): DNBSEQ-G50

ORGANISM(S): Trypanosoma brucei brucei

SUBMITTER: Mark Carrington

PROVIDER: E-MTAB-17235 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNAseq of primary human Adipose-derived Mesenchymal Stromal Cells stimulated for 2 days with 20ng/mL IFN-gamma (versus unstimulated control) in presence of 10 nM rapamycin or DMSO (at 1:10000 dilution) as vehicle control

Project description:In order to study the impact of rapamycin on AD-MSC under inflammatory or resting conditions, primary human Adipose-derived Mesenchymal Stromal Cells (AD-MSC) at passage 1 were plated at 1.5x10^4 in MEM-alpha, 5% Human Platelet Lysate, 1% Penicillin-Streptomycin and allowed to stand for 24h. The next day, AD-MSC were stimulated for 2 days (or not) with 20ng/mL IFN-gamma in presence of 10nM rapamycin (from 10.000X stock in DMSO) or DMSO (at 1:10000 dilution) as vehicle control. After 2 days, media were removed and RNA were extracted using RNeasy kit from QIAGEN with an on-column DNAse I digestion as manufacturer's instructions. RNA intergrity number were estimated on Agilent Bioanalyzer and were all above 9 before sequencing. Libraries and RNA sequencing were performed by the Beijing Genomics Institute (BGI)

2025-04-03 | E-MTAB-14215 | biostudies-arrayexpress

RNaseq of primary human OA chondrocytes alones or in transwell cocultures with primary human Adipose-derived Mesenchymal Stromal Cells, in presence of 10nM rapamycin or DMSO as vehicle control

Project description:The objective was to study the combined effects of rapamycin and primary human Adipose-derived Mesenchymal Stromal Cells (AD-MSC) on primary human OA chondrocytes (versus their effects separetely), in an in-vitro model that reproduce an intra-articular injection. For this purpose, P1 OA chondrocytes were seeded in 6-well plates (5x10^5 cells/well) in their proliferative medium for 24h. In parallel, P1 AD-MSC were seeded in 0.4 µm inserts (7.2x10^4) in their proliferative medium for 24h. The next days, all media were removed, cells were washed twice with PBS and media were replaced by miminal chondrogenic medium. Finally, OA chondrocytes were cocultured with AD-MSC (versus alone) in presence of 10nM rapamycin or DMSO (at 1:10000 dilution) as vehicle control for 3 days. At the end, media and inserts were removed and RNA of OA chondrocytes were extracted using RNeasy kit from QIAGEN with an on-column DNase I digestion as manufacturer's instructions. Because of poor quality RNA, one sample (25_DMSO_AD10) and his control (25_RA10_AD10) have been excluded from this analysis. Otherwise, all RNA integrity numbers were above 9 before libraries construction.

2025-04-03 | E-MTAB-14216 | biostudies-arrayexpress

Generation of zero-valent sulfur from dissimilatory sulfate reduction in sulfate-reducing microorganisms

Project description:Dissimilatory sulfate reduction (DSR) mediated by sulfate-reducing microorganisms (SRMs) plays a pivotal role in global sulfur, carbon, oxygen, and iron cycles since ~3.5 billion years ago. The canonical DSR pathway is believed to be sulfate reduction to sulfide. Herein, we report a new DSR pathway in phylogenetically diverse SRMs through which zero-valent sulfur (ZVS) is directly generated. We identified that approximately 8.9% of sulfate reduction was directed toward ZVS with S8 as a predominant product, and the ratio of sulfate-to-ZVS could be changed with SRMs’ growth conditions, particularly the medium salinity. Further coculturing experiments and metadata analyses revealed that DSR-derived ZVS supported the growth of various ZVS-metabolizing microorganisms, highlighting this new pathway as an essential component of the sulfur biogeochemical cycle

2023-04-28 | PXD040825 | Pride

Differential protein expression between ESCC and normal tissues

Project description:To understand the difference of protein expression between paired esophageal squamous cell carcinoma (ESCC) and adjacent normal tissues, we collected 10 paired ESCC and normal tissues from surgical resected specimems for high-throughput proteomic experiments. From comparative analysis, the dysregulated signaling pathways in ESCC could be uncovered.

2020-08-11 | PXD019834 | Pride

RNA-seq of H3.3 knockout and wild type chicken DT40 cells

Project description:RNA-seq was performed for transcriptional analysis of wild-type DT40 cells (Gallus gallus, B-cell line) and a H3.3 knockout line (h3.3a-/-, h3.3b-/-). H3.3 is a H3 histone variant encoded on two genes (H3.3A and H3.3B) in chickens.

2014-08-31 | E-MTAB-2754 | biostudies-arrayexpress

RNA-sequencing of scrambled control CIN 612 cells and CIN 612 cells depleted of senataxin (SETX) through stable expression of shRNAs

Project description:HPV 31 positive cervical keratinocytes (CIN 612 cells) were transduced with lentiviruses to stably express either a scramble control sequence (Scrm CIN 612) or shRNAs targeting the RNA helicase, senataxin (SETX). RNA sequencing was performed on these cell lines to identify cellular genes whose expression was regulated by SETX expression. The experiment was done in biological duplicate, and two different shRNA sequences were used (shSETX1/13 and shSETX2/30).

2025-11-15 | E-MTAB-15997 | biostudies-arrayexpress

Deletion of ISG65 loci in Trypanosoma brucei

Project description:ISG65 null trypanosomes were produced to investigate the function of ISG65 in mammalian hosts.

2021-12-13 | E-MTAB-10878 | biostudies-arrayexpress

RNA-seq of Escherichia coli MG1655 and Salmonella Typhimurium SL1344 wild-types and their respective AcrB D408A mutants in LB broth, in stationary phase

Project description:This experiment was designed to find differences and similarities between the loss-of-AcrB-efflux-function mutants of two Enterobacterales, in stationary phase. Cultures were grown in LB broth for 10 hours. Four biological replicates per strain were analysed.

2021-03-04 | E-MTAB-8352 | biostudies-arrayexpress

N-hydroxy-pipecolic acid mediated priming of salicylic acid signalling in Arabidopsis thaliana

Project description:N-hydroxy-pipecolic acid (NHP) primes Aarabidopsis thaliana to confer faster and stronger activation of immune responses, but how NHP interacts with other immune-inducing phytohormones is unknown. Here we investigated the crosstalk between priming phytohormone NHP and immune inducing phytohormone salicylic acid (SA). We show that pretreatment with NHP modulates the SA-inducible transcriptome, wherein some SA-expressed genes show enhanced SA-sensitivity and some show reduced SA-sensitivity. 12 day old wild type (col-0) seedlings grown on MS media were treated with 1mM NHP or water overnight, then 0.5mM SA or water for 6 hours by immersion in 10ml of the respective chemicals. ~50 seedlings were pooled into one biological repeat, with three biological repeats total for this experiment. Seedlings were patted dry with tissue paper and frozen in liquid nitrogen for RNA extraction.

2024-12-25 | E-MTAB-14631 | biostudies-arrayexpress

Azelaic acid mediated priming of salicylic acid signalling in Arabidopsis thaliana

Project description:Azelaic acid (AzA) is a candidate systemic resistance inducing phloem mobile signal in Aarabidopsis thaliana, but whether it interacts with immune signalling and how is not known. Here we investigated the crosstalk between phloem signal AzA and immune inducing phytohormone salicylic acid (SA). We show that pretreatment with AzA modulates the SA-inducible transcriptome, wherein some SA-expressed genes show enhanced SA-sensitivity, but many more show reduced SA-sensitivity. 12 day old wild type (col-0) seedlings grown on MS media were treated with 1mM AzA or 5mM MES overnight, then 0.5mM SA or 5mM MES for 6 hours by immersion in 10ml of the respective chemicals. ~50 seedlings were pooled into one biological repeat, with three biological repeats total for this experiment. Seedlings were patted dry with tissue paper and frozen in liquid nitrogen for RNA extraction.

2024-12-25 | E-MTAB-14632 | 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