{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Daniel Humphreys"],"study_type":["transcription profiling by array"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15046"],"description":["Aim of the experiment: To examine changes in gene expression in HT1080 fibroblasts following treatment with purified recombinant wild-type typhoid toxin (WT-tox) from Salmonella Typhi relative to a mutant H160Q variant lacking DNase activity (HQ-tox), in the presence and absence of serum. The toxin causes DNA damage in both G0/G1 phase and G2/S phase of the cell cycle. Serum-starvation results in host cell cycle arrest in G0/G1 phase, meaning that DNA damage in G2/S is not permissive in the absence of serum. This experiment aimed to uncouple toxin-induced host transcriptomic responses to DNA damage in G0/G1 and G2/S phases of the host cell cycle. Experimental workflow: HT1080 fibroblasts were seeded one day before intoxication into T75 tissue culture flasks for a 30% confluency in DMEM with 1% PenStrep. Cells to be intoxicated in the presence of serum were supplemented with 10% foetal bovine serum (FBS), whereas no FBS was added for serum-starved cells. The next day, cells were incubated for 2h with WT-tox (5 ng/ml) or negative control HQ-tox (5 ng/ml) followed by three washes with PBS and a 48h chase in DMEM supplemented with 1% PenStrep and with or without 10% FBS as appropriate. After 48 h, cells were collected by trypsinisation. RNA was isolated and samples analysed using a human Clariom S assay (ThermoFisher Scientific, 902927). Analysis was performed with Transcriptome Analysis Console 4.0 software (Applied Biosystems, Thermo Fisher Scientific)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - HT1080 fibroblasts were seeded one day before intoxication into T75 tissue culture flasks for a 30% confluency in DMEM with 1% PenStrep. Cells to be intoxicated in the presence of serum were supplemented with 10% foetal bovine serum (FBS), whereas no FBS was added for serum-starved cells. The next day, cells were incubated for 2h with WT-tox (5 ng/ml) or negative control HQ-tox (5 ng/ml) followed by three washes with PBS and a 48h chase in DMEM supplemented with 1% PenStrep and with or without 10% FBS as appropriate. After 48 h, cells were collected by trypsinisation.","Labeling - cDNA was synthesised from 100ng RNA of total RNA using the GeneChip WT PLUS Reagent Kit. The cDNA was then fragmented and biotin-labelled using the GeneChip WT Terminal Labelling Kit according to the manufacturer's instructions (ThermoFisher)","Scaning - Scanning was done in the Affymetrix® GeneChip Scanner 3000 7G with autoloader. The GeneChip Operating Software (GCOS) software (ThermoFisher) was used to acquire and feature extract the data.","Nucleic Acid Extraction - Total RNA was extracted using the Qiagen RNeasy kit according to manufacturer's instructions.","Hybridization - Hybridisation and washing was done using the GeneChip™ Hybridization, Wash, and Stain Kit (ThermoFisher). Hybridisation was to GeneChip Clariom S Arrays for 16h at 60rpm and 45C. Washing and staining was done on an Affymetrix Fluidics Station 450."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","Processed Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Daniel Humphreys"],"data_protocol":["Data Transformation - Analysis was performed using Transcriptome Analysis Console 4.0 software (Applied Biosystems, ThermoFisher)."],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome of human HT1080 cells treated with purified typhoid toxin in the presence and absence of serum","description":"Aim of the experiment: To examine changes in gene expression in HT1080 fibroblasts following treatment with purified recombinant wild-type typhoid toxin (WT-tox) from Salmonella Typhi relative to a mutant H160Q variant lacking DNase activity (HQ-tox), in the presence and absence of serum. The toxin causes DNA damage in both G0/G1 phase and G2/S phase of the cell cycle. Serum-starvation results in host cell cycle arrest in G0/G1 phase, meaning that DNA damage in G2/S is not permissive in the absence of serum. This experiment aimed to uncouple toxin-induced host transcriptomic responses to DNA damage in G0/G1 and G2/S phases of the host cell cycle. Experimental workflow: HT1080 fibroblasts were seeded one day before intoxication into T75 tissue culture flasks for a 30% confluency in DMEM with 1% PenStrep. Cells to be intoxicated in the presence of serum were supplemented with 10% foetal bovine serum (FBS), whereas no FBS was added for serum-starved cells. The next day, cells were incubated for 2h with WT-tox (5 ng/ml) or negative control HQ-tox (5 ng/ml) followed by three washes with PBS and a 48h chase in DMEM supplemented with 1% PenStrep and with or without 10% FBS as appropriate. After 48 h, cells were collected by trypsinisation. RNA was isolated and samples analysed using a human Clariom S assay (ThermoFisher Scientific, 902927). Analysis was performed with Transcriptome Analysis Console 4.0 software (Applied Biosystems, Thermo Fisher Scientific).","dates":{"release":"2025-06-01T00:00:00Z","modification":"2025-04-17T10:02:22.188Z","creation":"2025-04-17T10:02:22.188Z"},"accession":"E-MTAB-15046","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"]}}