{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Julie COCQUET"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14570"],"description":["The aim of the experiment is to determine the consequences of the loss of Zfy1 and/or Zfy2 on gene expression at three stages of male germ cell differentiation: primary spermatocytes (SC1), secondary spermatocytes (SC2) and round spermatids (RS)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - RNA was extracted from each SC1, SC2, and RS cell fraction using the RNeasy Micro Kit (Qiagen, Hilden, Germany).","Library Construction - The cDNA libraries were prepared using the NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) before quality assessment with the Agilent Bioanalyzer.","Sample Collection - Primary spermatocytes (SC1), secondary spermatocytes (SC2), and round spermatid (RS) cells were isolated from wild type (XY), Zfy1 KO, Zfy2 KO, and Zfy DKO mice via germ cell isolation and fluorescence-activated cell sorting (FACS).","Sequencing - The Illumina NextSeq 2000 P3 flow cell (Illumina, San Diego, CA) was then used to perform paired-end sequencing of 150-bp reads (roughly 33 million reads for each sample)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - FASTQ files were trimmed and filtering using BBduk (v38.23) and were aligned with STAR (v2.7.2d) on the mouse genome (GRCm38.p6). STAR and samtools package (v1.3.1) were used to estimate raw read counts."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 2000"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Julie COCQUET"],"additional_accession":[]},"is_claimable":false,"name":"RNA-seq on Zfy Knock-out male germ cells","description":"The aim of the experiment is to determine the consequences of the loss of Zfy1 and/or Zfy2 on gene expression at three stages of male germ cell differentiation: primary spermatocytes (SC1), secondary spermatocytes (SC2) and round spermatids (RS).","dates":{"release":"2025-09-01T00:00:00Z","modification":"2025-09-02T00:02:11.726Z","creation":"2024-10-31T22:28:32.623Z"},"accession":"E-MTAB-14570","cross_references":{"ENA":["ERP165680"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}