{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Lukas Wijaya"],"organism":["Rattus norvegicus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-11969"],"description":["The data contains the transcriptomic responses of the nephron segments (CPT : cortical proximal tubules and PPT : Perimedular proximal tubules) of the rat kidneys exposed to single administration of cisplatin i.v. 5 mg/kg for 29 days (1, 3, 5, 8, 10, 12, 15, 20, 28 days of collection times). The kidneys were fixed with formaldehyde and embedded in paraffin followed by sectioning for 8 um thickness and staining with hematoxylin and eosin staining. The nephron segments were collected using laser capture microdissection microscope for targeted RNA sequencing purposes. The whole kidneys were taken along for the comparison. This RNAseq outcomes suggest different temporal dynamics of transcriptomic responses elicited in different nephron segments upon cisplatin exposure. This RNA-seq outcomes is the first technical replicate of the RNA sequencing. This is part of the TransQST project."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The kidneys were fixed with formaldehyde and embedded in paraffined. Prior to the collection, the kidneys were sectioned with 8 um thickness in a PEN membrane for laser capture microdissection purposes. On the collection day, the sections were stained with H&E staining and the regions of interest were collected. The samples were collected until reaching a total of ~200000 micrometer square of the surface area. The collected samples were frozen at -80'C until sequencing process.","Nucleic Acid Extraction - All the processes were according to BioSpyder-BioClavis protocol.","Sequencing - All the processes were according to BioSpyder-BioClavis protocol.","Library Construction - All the processes were according to BioSpyder-BioClavis protocol."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The .txt files contain the raw count values processes from the fastq files performed by BioClavis."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500","PALM Robo LCM"],"study_type":["RNA-seq of coding RNA"],"species":["Rattus norvegicus"],"pubmed_authors":["Lukas Wijaya"],"additional_accession":[]},"is_claimable":false,"name":"Transcriptomic Responses of Laser Capture Microdissected Nephrons from Rat Kidneys Exposed to Single administration of 5 mg/kg Cisplatin : 29 days study - first technical replicate of the RNA sequencing","description":"The data contains the transcriptomic responses of the nephron segments (CPT : cortical proximal tubules and PPT : Perimedular proximal tubules) of the rat kidneys exposed to single administration of cisplatin i.v. 5 mg/kg for 29 days (1, 3, 5, 8, 10, 12, 15, 20, 28 days of collection times). The kidneys were fixed with formaldehyde and embedded in paraffin followed by sectioning for 8 um thickness and staining with hematoxylin and eosin staining. The nephron segments were collected using laser capture microdissection microscope for targeted RNA sequencing purposes. The whole kidneys were taken along for the comparison. This RNAseq outcomes suggest different temporal dynamics of transcriptomic responses elicited in different nephron segments upon cisplatin exposure. This RNA-seq outcomes is the first technical replicate of the RNA sequencing. This is part of the TransQST project.","dates":{"release":"2025-07-15T00:00:00Z","modification":"2025-07-14T10:01:06.362Z","creation":"2022-08-01T18:35:33.619Z"},"accession":"E-MTAB-11969","cross_references":{"ENA":["ERP139724"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003816","EFO_0005518","EFO_0003738","EFO_0004184"]}}