biostudies-arrayexpressKai FangHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14538CAFs were indirectly co-cultured with SK-BR-3 or MDA-MB-231 cells (CAFs, ZQY042, Zhongqiao Xinzhou Biotechnology Co., Ltd.) for one week using a 0.4um transwell chamber, after which the CAFs were harvested. FITC anti-human CD133 antibody (W6B3C1, BioLegend) was used to sort CD133- and CD133+ cells by Fluorescence activated cell sorting (FACS).biostudies-arrayexpressSample Collection - CAFs were indirectly co-cultured with SK-BR-3 or MDA-MB-231 cells (CAFs, ZQY042, Zhongqiao Xinzhou Biotechnology Co., Ltd.) for one week using a 0.4um transwell chamber, after which the CAFs were harvested. FITC anti-human CD133 antibody (W6B3C1, BioLegend) was used to sort CD133- and CD133+ cells by Fluorescence activated cell sorting (FACS).Sequencing - Sequencing was outsourced to Novogene, targeting 20,000 paired reads per cell on an Illumina NovaSeq 2000 platform.Library Construction - The cDNA was then amplified via PCR for 11 cycles and further purified with SPRIselect magnetic beads. For library preparation, 25% of the cDNA yield was used. Library quality was assessed on the Agilent TapeStation 4200, and yield was quantified by qPCR with the KAPA Library Quantification Kit.Nucleic Acid Extraction - The process started with loading cells, gel beads, and partitioning oil onto a Chromium Next GEM Chip, aiming to recover approximately 10,000 cells per sample. The chip was processed in a Chromium Controller to create Gel Beads-in-Emulsion (GEMs). Reverse transcription was performed using the GEM-RT protocol on a PCR cycler. Following this, the GEMs were disrupted with Recovery Agent, and the cDNA was purified using DynaBeads MyOne Silane beads.OrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - naUnknownTranscriptomicsGenomicsProteomicsAgilent TapeStation 4200Illumina HiSeq 2000RNA-seq of coding RNA from single cellsHomo sapiensKai FangfalseCancer associated fibroblasts (CAFs), CD133- (SK-BR-3 and MDA-MB-231 mixed) and CD133+ cells (SK-BR-3 and MDA-MB-231 mixed)CAFs were indirectly co-cultured with SK-BR-3 or MDA-MB-231 cells (CAFs, ZQY042, Zhongqiao Xinzhou Biotechnology Co., Ltd.) for one week using a 0.4um transwell chamber, after which the CAFs were harvested. FITC anti-human CD133 antibody (W6B3C1, BioLegend) was used to sort CD133- and CD133+ cells by Fluorescence activated cell sorting (FACS).2025-09-30T00:00:00Z2025-09-30T01:04:50.887Z2024-10-16T10:47:29.597ZE-MTAB-14538EFO_0002944EFO_0004170EFO_0005684EFO_0005518EFO_0003816EFO_0004184