{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Dhanya Ramachandran"],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14356"],"description":["We aimed to identify specific targets of alternative splicing and gene expression patterns in fetal ECFCs. We performed transcriptome-wide differential splicing and gene expression analyses between cord blood ECFCs from preeclamptic (n=16) and normal pregnancies (n=13)."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was purified from ECFC lysates using the RNeasy Plus Mini Kit (Qiagen, Hilden, Germany).","Sample Collection - We centrifuged umbilical cord blood and separated plasma for storage at -80°C. After density gradient centrifugation, the cord blood mononuclear cell fraction was plated at 5 x 107 cells/well on collagen coated 6-well plates ((BioCoat; Corning, USA) and incubated at 37 °C and 5 % CO2. Cells were grown with endothelial basal medium (EBM-2, Lonza, Basel, Switzerland) supplemented with 10% fetal bovine serum (FBS, Harvard Bioscience, Harvard Bioscience, Holliston, USA), 1% penicillin/streptomycin (P/S, Bio&Sell, Nürnberg, Germany) and recommended supplements. After 10 to 21 days, ECFC colonies appeared as adherent single layers of cobblestone-shaped cells. ECFC phenotype was confirmed by flow cytometry assessing CD31 (130-117-390; BD Biosciences San Jose, USA), CD45 (555483; BD Biosciences), CD133 (130-090-826; Miltenyi Biotec, Bergisch Gladbach, Germany) and the corresponding isotype controls.","Library Construction - rRNA was depleted and PolyA enriched without globin depletion. A strand-specific library was utilized with the protocol NEB Ultra Directional RNA.","Sequencing - Samples were sequenced on the NovaSeq PE50 platform. All samples were mapped to human reference genome hg38 and transcriptome Homo_sapiens.GRCh38.79.gtf using STAR aligner version 2.4.2a for mapping. All samples had minimum of 30 million reads after removing counts mapping to rRNA, pseudogenes and Hemoglobin."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Counts (filtered) were transformed into counts per million and expressed as Log2 value. Log2CPM were normalized using TMM (weighted trimmed mean of M−values (to the reference)."],"omics_type":["Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of total RNA"],"species":["Homo sapiens"],"pubmed_title":["Alternative splicing of CADM1 is associated with endothelial progenitor cell dysfunction in preeclampsia"],"pubmed_authors":["Thilo Dörk","Dhanya Ramachandran","Frauke von Versen-Höynck","Ricarda Welz, Dhanya Ramachandran, Bianca Schröder-Heurich, Katja Richter, Robert Geffers, Constantin S. von Kaisenberg, Thilo Dörk, Frauke von Versen-Höynck"],"additional_accession":[]},"is_claimable":false,"name":"Alternative splicing and gene expression patterns of fetal cord-blood derived Endothelial Colony Forming Cells (ECFCs) in normal and preeclamptic pregnancies","description":"We aimed to identify specific targets of alternative splicing and gene expression patterns in fetal ECFCs. We performed transcriptome-wide differential splicing and gene expression analyses between cord blood ECFCs from preeclamptic (n=16) and normal pregnancies (n=13).","dates":{"release":"2025-08-07T00:00:00Z","modification":"2024-08-12T20:39:50.166Z","creation":"2024-08-12T20:39:50.166Z"},"accession":"E-MTAB-14356","cross_references":{"ENA":["ERP163210"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009653","EFO_0005518","EFO_0003816","EFO_0004184"]}}