{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Raphael Carapito"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14991"],"description":["We extracted RNA from PBMCs of patient and 3 matched healthy donors to identify disease associated gene expression pathways"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - SMARTer® Stranded Total RNA-Seq Kit v2 (Takara, Otsu, Shiga, Japan)","Sequencing - paired-end (2x75bp) on NextSeq500 (Illumina, San Diego, CA)","Nucleic Acid Extraction - RNA was extracted sing RNeasy® Mini Kit and QIAamp® RNA Blood Mini Kit (Qiagen, Hilden, Germany)","Sample Collection - PBMC were isolated from total EDTA blood using density gradient centrifugation (Pancoll #P04-67500, PAN-Biotech GmbH, Aidenbach, Germany or Ficoll, CMSMSL01-01, Eurobio scientific, Courtaboeuf, France)"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Sequence Alignment - Sequence reads (minimum 43,9 Millions) were mapped to Homo sapiens hg19 using STAR (Dobin et al., 2013) to obtain a BAM (Binary Alignment Map) file. Quantification was processed by HTSeq-count (Anders et al., 2015).","Data Transformation - For each sample, quantification data were loaded with the EdgeR package (Robinson et al., 2010) in order to create an abundance matrix. A trimmed Mean of M-values normalization (TMM) was applied and counts were converted in cpm (Counts per Millions)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["NextSeq 500"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_authors":["Raphael Carapito"],"additional_accession":[]},"is_claimable":false,"name":"Comparison of transcriptomes in PBMCs between Griscelli-like patient and healthy controls by RNA-seq","description":"We extracted RNA from PBMCs of patient and 3 matched healthy donors to identify disease associated gene expression pathways","dates":{"release":"2025-04-27T00:00:00Z","modification":"2025-04-01T14:33:05.915Z","creation":"2025-04-01T14:33:05.915Z"},"accession":"E-MTAB-14991","cross_references":{"ENA":["ERP171060"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}