{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Thomas Lind"],"study_type":["transcription profiling by array"],"organism":["Rattus rattus"],"species":["Rattus rattus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15555"],"description":["Bisphenol A (BPA) is an endocrine disruptor and exposure to low doses in utero has been associated with the development of metabolic diseases.  Pregnant rats, Fischer 344/DuCrl, were exposed to BPA via their drinking water from gestational day 3.5 till  weaning on post natal day 22.Three dosing groups were used, 0 (n=18), 0.5 (n=12) or 50 (n=15) μg BPA/kg body weight/day and bone marrow (humerus bone) from pups born from unexposed and exposed dams were harvested at the age of 52 weeks. Bone marrow total RNA was extracted using the TRI Reagent (Sigma-Aldrich) and hybridized to Affymetrix GeneChip Rat Gene 2.1 ST Arrays."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Bone marrow were isolated from left humeri. Both epiphyses (including growth plates) were removed and marrow was flushed out with a syringe containing ice cold PBS followed by collection using centrifugation.","Labeling - 250 nanograms of total RNA from each sample were used to generate amplified and biotinylated sense-strand cDNA from the entire expressed genome according to the GeneChipTM WT PLUS Reagent Kit User Manual (P/N 703174, ThermoFisher Scientific Inc., Life Technologies, Carlsbad, CA 92008).","Scaning - GeneChipTM ST Arrays (GeneChipTM Rat Gene 2.1 ST Array Plate) were hybridized, washed, stained and finally scanned with the GeneTitanTM Multi-Channel (MC) Instrument, according to the GeneTitanTM Instrument User Guide for Expression Array Plates (PN 702933, ThermoFisher, Scientific Inc.,Life Technologies, Carlsbad, CA 92008 USA). The raw microarray data was normalized and pre-processed using the method IterPLIER. Only probes with a group average signal value above 1.0 (one) are analyzed. IterPLIER is a pm-gcbg method (background adjusting) that performs a PLIER estimation and iteratively discards non-correlating probe sets. Background signals are subtracted from the probe signals. Differential Expressed Gene lists are created using R/Bioconductor (http://www.r-project.org) and Limma package release 3.6 (no confounding factors included). Cut-off values for significant probes are set p-value < 0.05 (adjusted using Benjamini-Hochberg). No outlier effects were revealed by Quality Control (QC) plots using the RMA-sketch version of the robust multi-array average (RMA) method.","Hybridization - Total RNA was prepared and samples were hybridized to the Affymetrix GeneChipTM Rat Gene 2.1 ST Arrays at the Array and AnalysisFacility at Uppsala University.","Sample Treatment - Dams were exposed to Bisphenol A (BPA) via their drinking water directly from their arrival at GD 3.5 till sacrifice at weaning on PND 22. Bisphenol A (80-05-7, (CH3)2C(C6H4OH)2, ≥99% purity) (Sigma Aldrich) was dissolved in ethanol and subsequently diluted with well-flushed tap water to defined final concentrations (1% ethanol in the final solutions). We aimed for the doses 0.5 μg BPA/kg, BW/day (BPA0.5) and 50 μg BPA/kg BW/day (BPA50). BPA solutions were freshly made, changed, and consumption measured twice every week. Control dams were given well-flushed tap water containing 1 vol% ethanol (vehicle). The pups were exposed mainly through the 157 placenta in utero and via milk during lactation but may also have been exposed directly through drinking the water during the last days of lactation. The concentration of BPA in the solution was verified at the Division of Occupational and Environmental Medicine in Lund, Sweden.","Nucleic Acid Extraction - The pelleted marrow cells were extracted using the TRI Reagent® (Sigma-Aldrich)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Thomas Lind"],"additional_accession":[]},"is_claimable":false,"name":"One-color microarray of rat bone marrow in response to developmental bisphenol A exposure compared to unexposed controls","description":"Bisphenol A (BPA) is an endocrine disruptor and exposure to low doses in utero has been associated with the development of metabolic diseases.  Pregnant rats, Fischer 344/DuCrl, were exposed to BPA via their drinking water from gestational day 3.5 till  weaning on post natal day 22.Three dosing groups were used, 0 (n=18), 0.5 (n=12) or 50 (n=15) μg BPA/kg body weight/day and bone marrow (humerus bone) from pups born from unexposed and exposed dams were harvested at the age of 52 weeks. Bone marrow total RNA was extracted using the TRI Reagent (Sigma-Aldrich) and hybridized to Affymetrix GeneChip Rat Gene 2.1 ST Arrays.","dates":{"release":"2025-09-05T00:00:00Z","modification":"2025-09-05T14:25:54.259Z","creation":"2025-09-05T14:20:53.048Z"},"accession":"E-MTAB-15555","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003815","EFO_0003969"]}}