{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Bruno Simoes"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13720"],"description":["Vacuum-assisted biopsy (VAB) from normal breast tissue were obtained from women participating in the Breast Cancer - Anti-Progestin Prevention Study 1 (BC-APPS1). A baseline VAB was performed in the luteal phase of the menstrual cycle and a second VAB was performed after a 12-week anti-progestin (ulipristal acetate, daily 5mg oral tablet) treatment. For each VAB a small piece of breast tissue was snap frozen in theatre. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) and indexed PolyA libraries were prepared using 100ng of total RNA. Paired-end 75bp sequencing was carried out on a NextSeq 500 sequencer (Illumina Inc.)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Normal breast tissue cores obtained via Vacuum-Assisted Biopsy (VAB) with a 10G biopsy needle were snap frozen for RNA extraction.","Nucleic Acid Extraction - RNA was extracted using the RNeasy Plus Micro Kit (#74034, Qiagen) as described in the manufacturer’s handbook.","Library Construction - Indexed PolyA libraries were prepared using 100ng of total RNA and 15 cycles of amplification in the Agilent Sure Select Strand Specific RNA Library Prep Kit for Illumina Sequencing (Agilent Cat No: G9691B). Libraries were quantified by qPCR using a Kapa Library Quantification Kit for Illumina sequencing platforms (Kapa Biosystems Inc. Cat No: KK4873).","Sequencing - Paired-end 75bp sequencing was carried out by clustering 2.0 pM of the pooled libraries on a NextSeq 500 sequencer (Illumina inc.).","Sample Treatment - A baseline VAB was performed in the luteal phase of the menstrual cycle and a second VAB was performed after a 12-week anti-progestin (ulipristal acetate, daily 5mg oral tablet) treatment."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - The fastq files were processed with Nextflow (v19.10.0), nf-core/rnaseq (v1.3) and aligned using GRCh38v96 as reference.","Data Transformation - The fastq files were processed with Nextflow (v19.10.0), nf-core/rnaseq (v1.3). Differentially expressed gene analysis was performed with DESeq2 (1.26.0) with a multi-factor design formula that accounted for treatment and patient-ID."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_authors":["Bruno Simoes"],"additional_accession":[]},"is_claimable":false,"name":"RNA-sequencing of normal breast tissue samples before and after 12-week anti-progestin (ulipristal acetate) treatment","description":"Vacuum-assisted biopsy (VAB) from normal breast tissue were obtained from women participating in the Breast Cancer - Anti-Progestin Prevention Study 1 (BC-APPS1). A baseline VAB was performed in the luteal phase of the menstrual cycle and a second VAB was performed after a 12-week anti-progestin (ulipristal acetate, daily 5mg oral tablet) treatment. For each VAB a small piece of breast tissue was snap frozen in theatre. RNA was extracted using the RNeasy Plus Micro Kit (Qiagen) and indexed PolyA libraries were prepared using 100ng of total RNA. Paired-end 75bp sequencing was carried out on a NextSeq 500 sequencer (Illumina Inc.).","dates":{"release":"2025-09-08T00:00:00Z","modification":"2025-09-08T01:02:43.074Z","creation":"2024-01-19T17:50:58.851Z"},"accession":"E-MTAB-13720","cross_references":{"ENA":["ERP156757"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184","EFO_0003969"]}}