{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Boris Hejblum"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15066"],"description":["COVERAGE-Immuno is a project that aims to perform in-depth, repeated evaluation of immunological markers and RNA data in COVID-19 patients who are being treated at home, to learn more about the disease. The project is embedded in an existing randomised clinical trial, called COVERAGE, that is evaluating several experimental treatments for patients at home. COVERAGE Immuno will use a technological tool that makes it possible to study a wide range of biological pathways with simple blood sampling. Coupled with innovative data science approaches, the project will be able to identify the most relevant biomarkers associated with the progression of the disease and the response to treatment at the early stage of the COVID-19 disease."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - mRNA librairies were prepared by NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina for cotton prick samples.","Sample Collection - At D0, each patient was educated to self-sample by using the finger-prick at home. Hence, self-collected finger-stick capillary blood samples were harvested at D0, D1, D3, D5, D7, D9, D12, and D14. Cotton swabs were stored in freezers and then collected weekly by a nurse.","Sample Collection - Blood samples through venopuncture were realized by a nurse at D0, D7 and D14 by Tempsu tube.","Sequencing - Libraries were sequenced on Illumina HiSeq 2500 V4 system. The sequencing depth were about 50 million reads and the fragment length of 1x100bp.","Nucleic Acid Extraction - Total RNA was purified from whole blood using Tempus Spin RNA Isolation Kit (Invitrogen) and Globin mRNAs removed by GLOBINclear-Human Kit (Ambion). RNAs were then quantified with Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific) before to be controlled for quality on the Bioanalyzer (Agilent).","Library Construction - mRNA libraries were prepared by the TruSeq Stranded mRNA kit according to Illumina protocol for Tempus whole blood recover."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Gene expression data were normalized as counts per million (CPM).","Sequence Alignment - Quality control of the alignment was performed via MultiQC v1.13. After this control stage, Trimmomatic v17.0.11 was used  to trim reads from sequences below a threshold, trim adapters and trim reads smaller than a defined length. The reads were aligned to the v44 human reference transcriptome (GRCh38.p14 from GenCode) using Salmon v1.8.0 and quantified relative to annotation model \\\"hsapiens_gene_ensembl\\\" recovered from the R package biomaRt v2.58.0."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina HiSeq 2500"],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Self-Collected Finger-Prick Blood for Gene Expression Profiling: Unveiling Early Immune Responses in Mild COVID-19"],"pubmed_authors":["Boris Hejblum","Rodolphe Thiébaut, Edouard Lhomme, Hakim Hocini, Isabelle Pellegrin, Andrea Boizard-Moracchini, Alexandre Duvignaud, Maud Perpère, Mélanie Huchon, Mélanie Prague, Christine Lacabaratz, Mathieu Surenaud, Xavier Anglaret, Denis Malvy, Boris Hejblum, COVERAGE study group, and Yves Levy."],"additional_accession":[]},"is_claimable":false,"name":"Coverage-Immuno","description":"COVERAGE-Immuno is a project that aims to perform in-depth, repeated evaluation of immunological markers and RNA data in COVID-19 patients who are being treated at home, to learn more about the disease. The project is embedded in an existing randomised clinical trial, called COVERAGE, that is evaluating several experimental treatments for patients at home. COVERAGE Immuno will use a technological tool that makes it possible to study a wide range of biological pathways with simple blood sampling. Coupled with innovative data science approaches, the project will be able to identify the most relevant biomarkers associated with the progression of the disease and the response to treatment at the early stage of the COVID-19 disease.","dates":{"release":"2026-09-01T00:00:00Z","modification":"2026-09-01T01:01:00.425Z","creation":"2025-04-23T12:52:54.974Z"},"accession":"E-MTAB-15066","cross_references":{"ENA":["ERP171890"],"EFO":["EFO_0002944","EFO_0004170","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}