{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Juan Garcia"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16224"],"description":["To assess the regulation of trophoblast fusion by aPKC-ζ isoforms, PRKCZ-targetting siRNA was transfected into trophoblast stem cells CT29 cell lines which were subsequently used to generate placental organoids. A total of three control and 3 knockdown organoids were sequenced."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - CT29 cell lines were grown and treated with either PRKCZ-targetting siRNA or a scrambled control. The cell lines were used to generate placental organoids.","Growth Protocol - CT 29 lines were maintained on 5 µg/mL collagen IV coated plates and using human TSC culture medium in a humidified incubator at 37 degrees and 5% CO2. Organoids were generated using a rotatory cell culture system.","Library Construction - Bulk seq libraries were constructed using the Illumina Stranded mRNA Prep Kit.","Sample Treatment - CT29 knockdowns were achieved utilizing PRKCZ-targetting siRNA that was transfected into the cell line using Opti-MEM I Reduced Serum Medium and Lipofectamine LTX Reagent with PLUS reagent.","Sequencing - Partial lane sequencing was performed via Illumina next generation sequencing (NovaSeq X Plus Series PE150) for 100M read pairs per sample","Nucleic Acid Extraction - Placental organoids were pelleted and resuspended in trizol before being mechanically dissociated utilizing a tissue lyser. RNA was extracted by utilizing Invitrogen PureLink RNA Mini Kit."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Bulk seq libraries were quality processed and trimmed utilizing the FASTQC pipeline. Trimmed sequenced were mapped to GRCh38/hg38 utilizing STAR v2.7.11","Data Transformation - Data was extracted in Ubuntu utilizing FeatureCounts. Data was analyzed utilizing the DESeq2 package in R."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Meghan Riddell","Sumaiyah Shaha","Juan Garcia","Bethan Wilson","Ivan Domingo"],"additional_accession":[]},"is_claimable":false,"name":"RNA seq of placental organoids generated from CT29 cell lines treated with PRKCZ-targetting siRNA versus control","description":"To assess the regulation of trophoblast fusion by aPKC-ζ isoforms, PRKCZ-targetting siRNA was transfected into trophoblast stem cells CT29 cell lines which were subsequently used to generate placental organoids. A total of three control and 3 knockdown organoids were sequenced.","dates":{"release":"2026-06-25T00:00:00Z","modification":"2026-06-25T16:11:31.65Z","creation":"2025-11-20T13:24:02.694Z"},"accession":"E-MTAB-16224","cross_references":{"ENA":["ERP185411"],"Biostudies":["E-MTAB-16225"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}