{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Kai Fang"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14538"],"description":["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)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample 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."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - na"],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Agilent TapeStation 4200","Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Kai Fang"],"additional_accession":[]},"is_claimable":false,"name":"Cancer associated fibroblasts (CAFs), CD133- (SK-BR-3 and MDA-MB-231 mixed) and CD133+ cells (SK-BR-3 and MDA-MB-231 mixed)","description":"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).","dates":{"release":"2025-09-30T00:00:00Z","modification":"2025-09-30T01:04:50.887Z","creation":"2024-10-16T10:47:29.597Z"},"accession":"E-MTAB-14538","cross_references":{"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}