GSM8841431: MDA-MB-231 parental cells, day 0; Homo sapiens; RNA-Seq
Cells were collected and counted using a hand-held Coulter counter (Scepter 3, Merck Millipore). Cells were diluted to a target concentration of approximately [1000 cells/µL] for optimal loading onto the 10x Genomics Chromium Controller. Single-cell suspensions were processed using the 10x Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (CG000315 REV E) according to the manufacturer's protocol. Cells were loaded onto the Chromium Controller to generate Gel Bead-In Emulsions (GEMs) containing individual cells, barcoded primers, and enzymes necessary for reverse transcription (PN-1000123, 10x Genomics). GEM generation and barcoding efficiency were monitored during the process to ensure high-quality libraries. GEMs were lysed to release cellular RNA, followed by reverse transcription and amplification to generate full-length cDNA (PN-1000190, 10x Genomics). cDNA libraries were fragmented, end-repaired, A-tailed, and ligated to sequencing adapters. Library quality and concentration were assessed using the Agilent Bioanalyzer 2100 (catalog) and Qubit dsDNA HS Assay Kit (catalog), respectively. Libraries were sequencing-ready after achieving a target fragment size of approximately [~500 bp]. ]. Library sequencing was done by Novogene (www.novogene.com) on an Illumina [NovaSeq 6000/NextSeq] platform using paired-end reads with a read length of 150 bp.