biostudies-arrayexpressJuan GarciaHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16224To 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.biostudies-arrayexpressSample 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 sampleNucleic 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.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesSequence Alignment - Bulk seq libraries were quality processed and trimmed utilizing the FASTQC pipeline. Trimmed sequenced were mapped to GRCh38/hg38 utilizing STAR v2.7.11Data Transformation - Data was extracted in Ubuntu utilizing FeatureCounts. Data was analyzed utilizing the DESeq2 package in R.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina NovaSeq XRNA-seq of coding RNAHomo sapiensMeghan RiddellSumaiyah ShahaJuan GarciaBethan WilsonIvan DomingofalseRNA seq of placental organoids generated from CT29 cell lines treated with PRKCZ-targetting siRNA versus controlTo 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.2026-06-25T00:00:00Z2026-06-25T16:11:31.65Z2025-11-20T13:24:02.694ZE-MTAB-16224ERP185411E-MTAB-16225EFO_0002944EFO_0004170EFO_0003789EFO_0004917EFO_0005518EFO_0003816EFO_0003738EFO_0004184EFO_0003969