{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;ILLUMINA, NextSeq 500;ILLUMINA"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001003705"],"sample_count":["32"],"description":["EGA dataset EGAD00001003705"],"repository":["EGA"],"title":["Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics"],"pubmed_abstract":["The human placenta is a dynamic and heterogeneous organ critical in the establishment of the fetomaternal interface and the maintenance of gestational well-being. It is also the major source of cell-free fetal nucleic acids in the maternal circulation. Placental dysfunction contributes to significant complications, such as preeclampsia, a potentially lethal hypertensive disorder during pregnancy. Previous studies have identified significant changes in the expression profiles of preeclamptic placentas using whole-tissue analysis. Moreover, studies have shown increased levels of targeted RNA transcripts, overall and placental contributions in maternal cell-free nucleic acids during pregnancy progression and gestational complications, but it remains infeasible to noninvasively delineate placental cellular dynamics and dysfunction at the cellular level using maternal cell-free nucleic acid analysis. In this study, we addressed this issue by first dissecting the cellular heterogeneity of the human placenta and defined individual cell-type-specific gene signatures by analyzing more than 24,000 nonmarker selected cells from full-term and early preeclamptic placentas using large-scale microfluidic single-cell transcriptomic technology. Our dataset identified diverse cellular subtypes in the human placenta and enabled reconstruction of the trophoblast differentiation trajectory. Through integrative analysis with maternal plasma cell-free RNA, we resolved the longitudinal cellular dynamics of hematopoietic and placental cells in pregnancy progression. Furthermore, we were able to noninvasively uncover the cellular dysfunction of extravillous trophoblasts in early preeclamptic placentas. Our work showed the potential of integrating transcriptomic information derived from single cells into the interpretation of cell-free plasma RNA, enabling the noninvasive elucidation of cellular dynamics in complex pathological conditions."],"pubmed_title":["Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics."],"pubmed_authors":["Tsang Jason C H JCH, Vong Joaquim S L JSL, Ji Lu L, Poon Liona C Y LCY, Jiang Peiyong P, Lui Kathy O KO, Ni Yun-Bi YB, To Ka Fai KF, Cheng Yvonne K Y YKY, Chiu Rossa W K RWK, Lo Yuk Ming Dennis YMD"],"pubmed_title_synonyms":["Fresh, Ribonucleic, d230, Fresh Frozen Plasma, Blood, Gene Expression., Gene, dTAFII250, EfW1, Gene Expression Profilings, dmTAF[[II]]230, Transcript Expression Analysis, mRNA Differential Displays, Gene Expression Pattern Analysis, dmTAF1, Taf230, Gene Products, Gene Expression Monitorings, Analysis, Profilings, Non Polyadenylated, RNA Gene Products, TAF250, Fresh Frozen Plasmas, Fresh Frozen, Taf200, Blood Plasma, dTAF[[II]]250, TFIID TAF250, Analyses, cel, cell, Taf1p, Transcriptomics, Transcript Expression, Transcriptome Analysis, Monitoring, Non-Polyadenylated RNA, dTAF250, Gene Expression Analysis, Blood Plasmas, TAF, Expression Analyses, plasma, Profiling, RNA, dTAF[[II]]230, TAF[[II]]250, Frozen Plasma, Transcriptome, ribose nucleic acid, ribonucleic acids, TAF200, Monitorings, l(3)84Ab, RNS, BG:DS00004.13, TAFII-250, TAF250/230, Plasmas, Cell, dTAF230, Frozen Plasmas, Gene Expression, Differential Display, TAFII250, Transcript Expression Analyses, p230, yeast nucleic acid, Ribonukleinsaeure, TAF[[II]]250/230, TFIID, pentosenucleic acids, Ribonucleic acids, mRNA Differential Display, Taf[[II]]250, Plasma, ribonucleic acid, Acid, Gene Expression Monitoring, TAF[[II]]230, Transcriptome Profiling, mRNA, Transcriptome Profilings, Non Polyadenylated RNA, Non-Polyadenylated, portion of plasma, TAF[II]250, Ribonucleic Acid, Differential Displays, CG17603, TAF[[II]], Transcriptome Analyses, DmelCG17603, Gene Expression Analyses, Taf250, SR3-5, Expression Analysis, TAF230, TAF1"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_abstract_synonyms":["concomitant conditions, MGC130048, Proteinuria Edema Hypertension Gestosis, Ribonucleic, scale tissue, Materials, determination, acetylglucosaminyltransferase-like protein, Blood, placenta (Spanish, Mbp1, A4, cfDNA, Circulating, Proteinuria-Edema-Hypertension, Circulating DNA, element, ter, dmTAF[[II]]230, PREGN, exact), Cell-Free, 1, Preeclampsia, Cell-Free Nucleic Acid, placenta, Fs(3)Hor, myd, Non Polyadenylated, Cell Free Nucleic Acid, RNA Gene Products, organ, gamma sarcoglycan, Fresh Frozen Plasmas, Fresh Frozen, DmelCG2684, cirDNA, Man (Taxonomy), TFIID TAF250, like-acetylglucosaminyltransferase, cel, associated disease, plant peltate hair, Tissue, Mbp-1, NTef2, 1s, Toxemia Of, acidos nucleicos, Bsg75C, Normal, sequelae, gamma-sarcoglycan, eutherian placenta, plasma, dTAF[[II]]230, placentas (exact, Frozen Plasma, Data Set, ribose nucleic acid, gyltl1b-b, Of Pregnancies, plural), concomitant disease, Modern, Arts, ribonucleic acids, SG-gamma, TAF200, Extravillous, EPH Toxemias, TAFII-250, TAF250/230, Plasmas, EPH Gestosis, Fs(3)Sz11, Cell Free Ribonucleic Acid, Eclampsia 1, TAFII250, nucleic acids, Term, MDDGA6, Ribonukleinsaeure, mKIAA0609, pentosenucleic acids, Genetic Materials, sarcoglycan, simple tissue, Ribonucleic acids, Circulating Nucleic Acids, Cell-Free Deoxyribonucleic Acid, Of Pregnancy, toxemia of pregnancy, KIAA0609, Genetic Material, acetylglucosaminyltransferase-like 1A, Proteinuria-Edema-Hypertension Gestosis, Pre Eclampsia, fg, Acid, sequels, Edema Proteinuria Hypertension Gestosis, Industrial, gyltl1b, Industrial Arts, Circulating Cell Free Nucleic Acids, Syncytiotrophoblast, Cytotrophoblasts, Cell Free Nucleic Acids, Nucleic Acids, Toxemia Of Pregnancies, mdc1d, INSDC_feature:gene, CG17603, gamma (35kDa dystrophin-associated glycoprotein), TAF[[II]], LARGE_HUMAN, human, Nucleic, early, MDC1D, Eclampsia 1s, DMDA, Hypertension Edema Proteinuria Gestosis, enr, Taf250, Material, SR3-5, 35kD dystrophin-associated glycoprotein, Horka, Placentomes, CG2684, Fs(3)Horka, Cistron, Acids, DNA, EPH, TAF230, hypertension, Fresh, Pregnancy Toxemias, d230, human being, coexistent disease, SGCG_HUMAN, Fresh Frozen Plasma, Cell-Free Deoxyribonucleic, Trophoblast, Circulating Cell Free Nucleic Acid, peltate hair, Extravillous Trophoblast, Gene, dTAFII250, EfW1, LARGE1, TYPE, Pregnancies, froggy, Gyltl1a, Human, DAGA4, Circulating Cell-Free Nucleic Acid, acides nucleiques, Microfluidic, Homo sapiens, Deoxyribonucleic Acid, dmTAF1, Taf230, coexistent conditions, Cell-Free RNA, 35DAG, Gene Products, DmF2, Pregnancy Toxemia, Cell Free DNA, MAM, gamma-SG, Hypertension-Edema-Proteinuria Gestosis, SCG3, Man, Edema-Proteinuria-Hypertension Gestosis, TAF250, lod, Preeclampsia Eclampsia 1, study, trophoderm, Taf200, Cell Free Deoxyribonucleic Acid, Blood Plasma, Edema-Proteinuria-Hypertension, trophoblast layer, dTAF[[II]]250, Genetic, cell, MDDGB6, dysfunction, Taf1p, LARGE, Maintenances, Preeclampsia Eclampsia 1s, Cell-Free Ribonucleic, Circulating Cell-Free Nucleic Acids, RNA Gene Products., 胎座 (Japanese, Non-Polyadenylated RNA, dTAF250, BPFD#36, portion of placenta tissue (exact), Toxemia Of Pregnancy, DmelCG4216, anatomical unit, Blood Plasmas, body organ, Pregnancy, Gestosis, TAF, trophoblastus, RNA, TAF[[II]]250, 35 kDa dystrophin-associated glycoprotein, acide nucleique, Placentas, Syncytiotrophoblasts, l(3)84Ab, RNS, BG:DS00004.13, Cistrons, Cell, SGCG, LGMD2C, dTAF230, Circulating RNA, Frozen Plasmas, placentae (exact, Toxemias, massa cellularis externa, Circulating Nucleic Acid, p230, Nucleic Acid, yeast nucleic acid, chemical analysis, TAF[[II]]250/230, EPH Complex, TFIID, NA, scales, Cell Free RNA, Cell-Free DNA, Taf[[II]]250, Plasma, Toxemia, ribonucleic acid, TAF[[II]]230, Nukleinsaeure, DMDA1, scale, Gestation, Non Polyadenylated RNA, allantoic placenta, Non-Polyadenylated, CG4216, Cytotrophoblast, portion of plasma, cirRNA, TAF[II]250, acido nucleico, pathophysiology, Ribonucleic Acid, associated conditions, Lds, cfRNA, Hypertension-Edema-Proteinuria, Circulating Nucleic, DmelCG17603, EPH Toxemia, toxaemia of pregnancy, like-glycosyltransferase, Cell-Free Ribonucleic Acid, Modern Man, Nukleinsaeuren, SCARMD2, Placentome, assay, Placentoma, glycosyltransferase-like protein LARGE1, TAF1, Preeclampsia Eclampsia"],"description_synonyms":["Ribonucleic, Reverse, BamF, biml, BamC, Blood, bam, Xkl-1, Probes, dmTAF[[II]]230, KL receptor activity, Gsfsco1, cDNA library construction, cromo, SCO5, SCO1, Software Engineering, DmelCG10422, Gsfsow3, Gsfsco5, CG18546, Non Polyadenylated, Computer Program, RNA Gene Products, SOW3, multicellular organismal biosynthetic process, Fresh Frozen Plasmas, Fresh Frozen, single-organism biosynthetic process, me75, 24Cr, Man (Taxonomy), TFIID TAF250, Genomes, cel, HCAP, Open, complementary DNA, Computer Programs and Programming, nucleic acid library preparation, W, CDLS3, D17Mit170, T1, BMH., Bs, cDNA Probes, s, Reagents, Sl, plasma, reagents, dTAF[[II]]230, Frozen Plasma, ribose nucleic acid, Cr, Modern, ribonucleic acids, TAF200, Tr-kit, RNA-seq, ham, 10x sequencing, TAFII-250, TAF250/230, Tl3, Plasmas, anon-WO03070958.3, Tl2, Source Softwares, Software Tools, Programs, PBT, Program, Computer Applications, chrome, TAFII250, Ribonukleinsaeure, Computer Applications Software, Computer Applications Softwares, kl1-A, pentosenucleic acids, Ribonucleic acids, Softwares, KIT, reactif, END, tyrosine-protein kinase Kit, Acid, pbt, Software Applications, Chrom, Source Software, reagent, kit, whole genome, alpha, CG17603, study protocol, TAF[[II]], human, Applications, BIM, Taf250, SR3-5, Indicator, SMC3L1, Complementary DNA, TAF230, krk1, Computer Software Applications, Fresh, d230, human being, bim, Fresh Frozen Plasma, Reagent, SCF receptor activity, dTAFII250, Computer, EfW1, aligned, Human, fs(3)neo61, CG10422, method, scfr, Homo sapiens, dmTAF1, Taf230, method used in an experiment, Gene Products, Whole Transcriptome Shotgun Sequencing, bim-beta7, Low, SCFR, Reagents and Indicators, Man, Application, TAF250, Open Source Softwares, Taf200, Fdc, Blood Plasma, Transcription, anatomical systems, dTAF[[II]]250, reactivo, cell, bim-beta6, Software Application, Open Source Software, nucleic acid library construction, Taf1p, Indicators, Computer Software Application, Non-Polyadenylated RNA, dTAF250, Tools, Blood Plasmas, TAF, 10X sequencing, CSPG6, HHT1, Applications Software, proto-oncogene c-Kit, Open Source, RNA, TAF[[II]]250, Computer Software, cou, Edg, synthesize, DmelCG31211, l(3)84Ab, aligned to, RNS, BOD, BG:DS00004.13, cDNA, Cell, Tool, dTAF230, Frozen Plasmas, Software Tool, Lr, KIT ligand receptor activity, p230, yeast nucleic acid, TAF[[II]]250/230, TFIID, bod, Software, Library, bimel, XKrk1, Taf[[II]]250, Plasma, ribonucleic acid, c-KIT, TAF[[II]]230, library construction, Non Polyadenylated RNA, Engineering, Non-Polyadenylated, portion of plasma, TAF[II]250, Ribonucleic Acid, CD117, CG14732, plan specification, Computer Programs, chromium, c-kit, DmelCG17603, Applications Softwares, C-Kit, Bam-C, Ssm, Modern Man, BAM, Bam, xkl-1, Bra, Chromium, ORW1, TAF1"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-DCPTCUHK-06-09-2017-12:56:47:296-247 - samples","description":"10 single-cell placental RNA libraries were generated using the Chromium Single Cell 3′ Reagent Kit (10X Genomics). All single-cell libraries were sequenced with a customized paired end with dual indexing (98/14/8/10-bp) format according to the recommendation by 10X Genomics. The data were aligned using the Cell Ranger Single-Cell Software Suite (version 1.0). Moreover, plasma RNA from 22 samples were extracted using the RNeasy Mini Kit (Qiagen). cDNA reverse transcription, second-strand synthesis, and RNA-sequencing (RNA-seq) library construction were performed using the Ovation RNA-seq System V2 (NuGEN) kit according to the manufacturer’s protocol. For alignment of the plasma RNA library, adaptor sequences and low-quality bases on the fragment ends (i.e., quality score < 5) were trimmed, and reads were aligned to the human reference genome (hg19) using the TopHat (v2.0.4) software. All aligned reads were deposited in bam file format.","dates":{"updated":"2020-07-16 15:33:08"},"accession":"EGAD00001003705","cross_references":{"TAXONOMY":["9606"],"pubmed":["28830992"],"EGA":["EGAC00001000078","EGAS00001002449"]}}