{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Aubry Marc"],"instrument_platform":["Illumina HiSeq 2000"],"study_type":["RNA-seq of coding RNA"],"organism":["Homo sapiens"],"species":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-11518"],"description":["Proteomics and transcriptomics data were integrated in order to identify hard-to-reach uncharacterized proteins which are known to be particularly numerous in human spermatozoa. MS-identifications were launched both against UniprotKB and translated predicted ORF databases generated from four different RNAseq processing workflows.  For each validated peptide-spectrum match (PSM), not identified in UniprotKB, but at least in one of the four customized databases, spectrum was carefully checked manually to assess the novel identification reliability."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Human testis RNA-seq was carried out on total RNA from normal human testis samples. Libraries were sequenced on a Illumina HiSeq 2000 instrument.","Library Construction - Libraries were prepared from 1 ug cDNA with the NEBNext Ultra II DNA kit and Index kit Set A (Biolabs). The final pool was quantified by Qubit dsDNA High Sensitivity kit (Thermofischer) at 45 nM and qualified with the Bioanalyzer at an average size of 359 bp. To correct the unbalanced base composition of the libraries prepared, we used a PhiX spike-in (15%).","Nucleic Acid Extraction - Total RNA was extracted using the NucleoSpin RNA XS Kit (Macherey Nagel) from 35 µL human spermatozoa cells. Quality control was realized on the RNA extracts with a 2100 bioanalyzer on chip Pico RNA (Agilent Technologies) to measure RNA Integrity Number then on nanodrop 2000 (Nanodrop) for the quantitative measurement. Reverse transcription and cDNA amplification were performed  with WTA2 kit (Sigma Aldrich) from 100 ng of total RNA according to the manufacturer’s instructions.","Sample Collection - Human semen samples were collected from healthy donors of unproven fertility at Nantes University Hospital (France)."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Aubry Marc","Emmanuelle Com","Guillot Laetitia"],"additional_accession":[]},"is_claimable":false,"name":"Integration of next-generation sequencing and proteomics data: application to the discovery of new coding events in the human spermatozoa","description":"Proteomics and transcriptomics data were integrated in order to identify hard-to-reach uncharacterized proteins which are known to be particularly numerous in human spermatozoa. MS-identifications were launched both against UniprotKB and translated predicted ORF databases generated from four different RNAseq processing workflows.  For each validated peptide-spectrum match (PSM), not identified in UniprotKB, but at least in one of the four customized databases, spectrum was carefully checked manually to assess the novel identification reliability.","dates":{"release":"2025-12-30T00:00:00Z","modification":"2025-12-30T02:02:03.849Z","creation":"2022-03-08T18:00:16.839Z"},"accession":"E-MTAB-11518","cross_references":{"ENA":["ERP136094"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"]}}