{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Frederic Lepretre"],"study_type":["transcription profiling by array"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15385"],"description":["The transgenic FVB/N 11.5kb-GFP mouse line was generated using the 11.5 kb s-SHIP promoter. During puberty, GFP expression in the mammary gland is specifically restricted to cap cells, which exhibit stem cell-like properties. To investigate the molecular basis underlying the differences between these basal GFP⁺ cap cells and other mammary epithelial subpopulations, we employed fluorescence-activated cell sorting to isolate four distinct mammary cell populations from 6-week-old mice, based on GFP expression in combination with CD24 and CD49f cell surface markers. These populations were subsequently analyzed for gene expression profiles."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - The transgenic FVB/N 11.5kb-GFP mouse line was generated using the 11.5 kb s-SHIP promoter. During puberty, GFP expression in the mammary gland is specifically restricted to cap cells, which exhibit stem cell-like properties. To investigate the molecular basis underlying the differences between these basal GFP⁺ cap cells and other mammary epithelial subpopulations, we employed fluorescence-activated cell sorting to isolate four distinct mammary cell populations from 6-week-old mice, based on GFP expression in combination with CD24 and CD49f cell surface markers.","Labeling - The cRNA was labeled, using the Low Input Quick Amp Labeling Kit  (Agilent Technologies, Santa Clara, CA, USA)  with Cyanine-3 (Cy3) according to the manufacturer's instructions.","Scaning - Slide was scanned with Agilent SureScan Microarray Scanner G2505C using one color scan setting for 8x60k array slides (028005_D_F_20130207). The image was scanned with Feature Extraction (version 10.7.3.1, Agilent Technology), using the default settings.","Nucleic Acid Extraction - Total RNA was isolated according to the manufacturer’s instructions (Macherey-Nagel) and assessed by the Agilent BioAnalyzer.","Hybridization - The hybridization and washing of the slides were performed according to the manufacturer’s protocols (Agilent Technologies; One-Color Microarray-Based Gene Expression Analysis)."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"pubmed_authors":["Frederic Lepretre"],"data_protocol":["Data Transformation - Raw data were then filtered for intensity and quality signal by using Agilent GeneSpring. Percentile Shift Normalization with default settings to 75th percentile settings were used. Probes with intensity values below 20th percentile were filtered out using the “Filter Probesets by Expression” option. Irregular signals or “compromised” features have been removed using the “filter by flags: detected; not detected” quality control option. .For this study, differentially expressed genes were identified according to the criteria: t-test unpaired p (Corr) cut-off = 0.05 with Benjamini Hochberg False Discovery Rate correction."],"additional_accession":[]},"is_claimable":false,"name":"Transcriptome profiling of mammary gland cell subpopulations isolated from the transgenic mouse model FVB 11.5-kb-GFP.","description":"The transgenic FVB/N 11.5kb-GFP mouse line was generated using the 11.5 kb s-SHIP promoter. During puberty, GFP expression in the mammary gland is specifically restricted to cap cells, which exhibit stem cell-like properties. To investigate the molecular basis underlying the differences between these basal GFP⁺ cap cells and other mammary epithelial subpopulations, we employed fluorescence-activated cell sorting to isolate four distinct mammary cell populations from 6-week-old mice, based on GFP expression in combination with CD24 and CD49f cell surface markers. These populations were subsequently analyzed for gene expression profiles.","dates":{"release":"2025-08-15T00:00:00Z","modification":"2025-07-22T13:35:32.133Z","creation":"2025-07-22T13:35:32.133Z"},"accession":"E-MTAB-15385","cross_references":{"EFO":["EFO_0002768","EFO_0002944","EFO_0003814","EFO_0003813","EFO_0005518","EFO_0003816","EFO_0003815"]}}