biostudies-arrayexpressHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14066Proof of principle and optimization experiment on cardioid with10X-based-iPS2-seq was performed on two batches of hPSC-derived cardioids at day 7.5 and pooled together after sample multiplexing. hPSC were primed and treated with Tetracycline 5 days prior cardiac differentiation. CG000388 Rev B (when multiplexing) User Guide was followed with sample multiplexing, provided information of the multiplexing for the cellranger aggr is provided. Sequencing has been performed on a Nextseq 1000 on a P2 Illumina kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles.biostudies-arrayexpressLibrary Construction - CG000388 Rev B (with cell multiplexing oligos). hPS-2seq barcode enrichment protocol was performed with custom primers binding on the TET repressor.Nucleic Acid Extraction - 10X genomics technology with CG000388 Rev B (with cell multiplexing oligos). Cells were loaded on a chip G.Sample Collection - Digestion with versene and trippleE. Then cells were labeled with CMO, sorted for vital cells and then loaded on the 10X controller.Sequencing - Nextseq 1000 P2 100 cycles. Cell multiplexing barcodes were pulled in molar ratio compared to the gen expression library 1:6. hPS2seq barcodes were pulled in molar ratio compared to the gen expression library 1:20.MINSEQE ScoreAssays and DataProcessed DataorganisationMAGE-TAB FilesData Transformation - Data provided are row. Use the atached aggregation.csv and config.csv files to run cell ranger aggr (aggregation.csv) and then cell ranger multi (config.csv)Data Transformation - shRNA information is atached to allow running CatcheR.Data Transformation - an RDS file is atached with the full processed data. Data can be read with readRDS() function in R and then it can be read and used with monocle 3. Additional txt files with data annotation and count data are provided to be analyzed with different platforms.MetabolomicsUnknownTranscriptomicsGenomicsProteomicsNextSeq 1000RNA-seq of coding RNA from single cellsHomo sapiensE-MTAB-14065Elisa BalmasfalseProof of principle for iPS2-10X-seq: cardioids experiment during 3D cardiac differentiationProof of principle and optimization experiment on cardioid with10X-based-iPS2-seq was performed on two batches of hPSC-derived cardioids at day 7.5 and pooled together after sample multiplexing. hPSC were primed and treated with Tetracycline 5 days prior cardiac differentiation. CG000388 Rev B (when multiplexing) User Guide was followed with sample multiplexing, provided information of the multiplexing for the cellranger aggr is provided. Sequencing has been performed on a Nextseq 1000 on a P2 Illumina kit 100 cycles. Sequencing run: Read1, 28 cycles; Index1, 10 cycles; Index2, 10 cycles, Read2, 90 cycles.2025-10-27T00:00:00Z2025-10-27T09:34:29.117Z2024-05-10T18:09:09.116ZE-MTAB-14066ERP160155E-MTAB-14065EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184