{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["thomas cokelaer"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"organism":["Leishmania donovani"],"species":["Leishmania donovani"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16528"],"description":["Leishmania parasites cycle between the sand fly as promastigotes and the mammalian host cells as amastigotes. Throughout their life cycle the parasites respond to external changes such as pH and temperature shifts or starvation that trigger differentiation from one stage to another. Such processes rely on several regulatory mechanisms occurring at different levels of gene expression including post-transcriptional and translational level. We applied high throughput RNA sequencing  on L. donovani amastigotes purified from the spleen of infected hamsters and the freshly derived promastigotes (after 2 passages in vitro) to investigate their respective transcriptomic signature. RNA was prepared from four biological replicates for each condition."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Libraries were constructed using a Illumina Stranded mRNA Prep (Illumina, USA) following the supplier's recommendations.","Sequencing - Libraries were constructed using a Illumina Stranded mRNA Prep (Illumina, USA) following the supplier's recommendations. RNA sequencing was performed on the Illumina NextSeq 2000 platform for a target of 40M paired-end reads per sample.","Sample Collection - Amastigotes were then recovered from the infected hamster spleens and used for nucleic acid and protein extractions. Promastigotes, derived from splenic amastigotes, were collected after 2 in vitro passages","Nucleic Acid Extraction - Total RNA was extracted from splenic amastigotes and promastigotes in exponential culture phase (4 biological replicates). Amastigotes and promastigotes were centrifuged respectively at 2,000 x g or 1,600 x g for 10 min at 4°C, and re-suspended in the lysis buffer supplied with the Qiagen RNeasy Plus kit. The samples were stored at -80°C and RNA extractions were performed according to the manufacturer’s instructions, including a DNase treatment."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Pascale Pescher","thomas cokelaer"],"additional_accession":[]},"is_claimable":false,"name":"Stage-specific analysis of L. donovani transcriptome","description":"Leishmania parasites cycle between the sand fly as promastigotes and the mammalian host cells as amastigotes. Throughout their life cycle the parasites respond to external changes such as pH and temperature shifts or starvation that trigger differentiation from one stage to another. Such processes rely on several regulatory mechanisms occurring at different levels of gene expression including post-transcriptional and translational level. We applied high throughput RNA sequencing  on L. donovani amastigotes purified from the spleen of infected hamsters and the freshly derived promastigotes (after 2 passages in vitro) to investigate their respective transcriptomic signature. RNA was prepared from four biological replicates for each condition.","dates":{"release":"2026-05-15T00:00:00Z","modification":"2026-05-15T01:00:42.026Z","creation":"2026-01-15T14:18:43.179Z"},"accession":"E-MTAB-16528","cross_references":{"ENA":["ERP187618"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}