{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Alper Eroglu"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16354"],"description":["Cell lines used to determine the growth of cell lines over time were used for transcriptomic profiling to build a model that predicts growth rate from transcriptome of cells.  To establish robust transcriptional signatures of dying cells, we performed single-well cell sorting followed by Smart-seq3xpress. 4T1, A549, MDA-MB-231 clone A, L and S were grown in cell culture medium. Adherent MDA-MB-231 clone L were grown with 1uM of Paclitaxel, a concentration we have previously shown to slow proliferation while retaining a viability compatible with the experiment27. The cells in culture were detached with Trypsin treatment for 3-5 minutes at 37 degrees C and the reaction was quenched by adding back the cells supernatant to conserve dead cells. The suspension was washed twice in PBS, 4 minutes at 400g. The cells were then labelled using the live/dead stain BOBO3 and apoptosis marker AnnexinV-APC following manufacturer's instruction. We isolated 3 cell populations on the basis of the BOBO3 and Annexin-V flow cytometry markers using an Aria3 flow cytometry with a 100um nozzle and low pressure settings. Live cells were gated as BOBO3- AnnexinV-, dying (early apoptotic) cells as BOBO3- AnexinV+ and dead cells (necrosis or late apoptosis) as BOBO3+ AnexinV+ (Fig. S2a-b). Individual cells were isolated in 384 well pcr-plates. After 10s centrifugation at 1000g the plates were sealed and stored at -80*C until processed using Smart-seq3xpress protocol30. All the reagents and bioinformatic pipeline related to Smart-seq3xpress are available online31."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The cell lines once in suspension were washed with PBS and pelleted by 5 minutes of centrifugation at 400g. The individual suspensions were filtered through a 35um mesh and their densities were adjusted to 106 cells/mL in PBS on ice. An equal volume of each suspension was pooled before being processed at the National Genomics Infrastructure (NGI, Scilifelab, Solna, Sweden).","Nucleic Acid Extraction - The cell lines once in suspension were washed with PBS and pelleted by 5 minutes of centrifugation at 400g. The individual suspensions were filtered through a 35um mesh and their densities were adjusted to 106 cells/mL in PBS on ice. An equal volume of each suspension was pooled before being processed at the National Genomics Infrastructure (NGI, Scilifelab, Solna, Sweden)","Growth Protocol - 4T1, A549, MDA-MB-231 clone A, L and S were grown in cell culture medium.","Library Construction - The cell lines once in suspension were washed with PBS and pelleted by 5 minutes of centrifugation at 400g. The individual suspensions were filtered through a 35um mesh and their densities were adjusted to 106 cells/mL in PBS on ice. An equal volume of each suspension was pooled before being processed at the National Genomics Infrastructure (NGI, Scilifelab, Solna, Sweden)","Sequencing - The cell lines once in suspension were washed with PBS and pelleted by 5 minutes of centrifugation at 400g. The individual suspensions were filtered through a 35um mesh and their densities were adjusted to 106 cells/mL in PBS on ice. An equal volume of each suspension was pooled before being processed at the National Genomics Infrastructure (NGI, Scilifelab, Solna, Sweden)","Sample Treatment - Adherent MDA-MB-231 clone L were grown with 1uM of Paclitaxel, a concentration we have previously shown to slow proliferation while retaining a viability compatible with the experiment"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Gene expression data from Smart-seq3 was normalized to 10,000 reads per cell - a figure often found in scRNAseq experiments - and subsequently log-transformed using the natural logarithm of (1 + x)."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Homo sapiens"],"pubmed_authors":["Alper Eroglu"],"additional_accession":[]},"is_claimable":false,"name":"In vitro growth signature identification from SmartSeq3 sequencing of 5 human cancer cell lines and 1 mouse cancer cell line","description":"Cell lines used to determine the growth of cell lines over time were used for transcriptomic profiling to build a model that predicts growth rate from transcriptome of cells.  To establish robust transcriptional signatures of dying cells, we performed single-well cell sorting followed by Smart-seq3xpress. 4T1, A549, MDA-MB-231 clone A, L and S were grown in cell culture medium. Adherent MDA-MB-231 clone L were grown with 1uM of Paclitaxel, a concentration we have previously shown to slow proliferation while retaining a viability compatible with the experiment27. The cells in culture were detached with Trypsin treatment for 3-5 minutes at 37 degrees C and the reaction was quenched by adding back the cells supernatant to conserve dead cells. The suspension was washed twice in PBS, 4 minutes at 400g. The cells were then labelled using the live/dead stain BOBO3 and apoptosis marker AnnexinV-APC following manufacturer's instruction. We isolated 3 cell populations on the basis of the BOBO3 and Annexin-V flow cytometry markers using an Aria3 flow cytometry with a 100um nozzle and low pressure settings. Live cells were gated as BOBO3- AnnexinV-, dying (early apoptotic) cells as BOBO3- AnexinV+ and dead cells (necrosis or late apoptosis) as BOBO3+ AnexinV+ (Fig. S2a-b). Individual cells were isolated in 384 well pcr-plates. After 10s centrifugation at 1000g the plates were sealed and stored at -80*C until processed using Smart-seq3xpress protocol30. All the reagents and bioinformatic pipeline related to Smart-seq3xpress are available online31.","dates":{"release":"2025-12-05T00:00:00Z","modification":"2026-05-27T12:44:42.95Z","creation":"2025-12-04T13:20:03.601Z"},"accession":"E-MTAB-16354","cross_references":{"ENA":["ERP186162"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}