{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["N/A"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001005448"],"sample_count":["78"],"description":["EGA dataset EGAD00001005448"],"repository":["EGA"],"title":["Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2"],"description_synonyms":["Materials, RNA Sequence Determination, determination, Sequence Determination, RNA Sequence, Mbp1, ScRNA seq, limitations, dmTAF[[II]]230, Techniques, neutrophilic leucocyte, single-cell RNA-seq, cromo, Method, neutrophil leukocyte, Ly-5, Seqs, Analysis, study limitations, myd, Non Polyadenylated, Seq, CD45R, me75, 24Cr, ScRNAseq, TFIID TAF250, Single-Cell Transcriptome Analysis, LY5, Analyses, cel, Determination, proportionality to, Comparative Genomics, Polyadenylated Messenger, Mbp-1, Dietary Fiber, Sequence Determinations, D17Mit170, T1, Methodological Studies, polymorphonuclear leukocyte, polynuclear neutrophilic leucocyte, B220, dTAF[[II]]230, Noise, Genomics, wide/broad, Polyadenylated, gyltl1b-b, Comparative, Single-Cell Gene Expression Profiling, Cr, TAF200, scRNA-seq, Pollution, RNA-seq, 10x sequencing, Functional Genomics, TAFII-250, Procedure, TAF250/230, Tl3, Tl2, Single-Cell, Determinations, chrome, neutrocyte, TAFII250, single cell RNA sequencing, MDDGA6, Lymphocyte antigen 5, mKIAA0609, 3.1.3.48, Genetic Materials, KIAA0609, Genetic Material, CD45, Polyadenylated Messenger RNA, fg, Single-Cell RNA, Non Polyadenylated mRNA, lymphocyte antigen 5, gyltl1b, protein_coding_transcript, Chrom, proportionality, mdc1d, expanded, rate, Methodological, CG17603, TAF[[II]], Single-Cell RNA Seq, Methodological Study, Non-Polyadenylated mRNA, MDC1D, wide, enr, Taf250, enlarged, Material, SR3-5, RNAseq, Cistron, Noise Pollution, T200, Poly(A) RNA, TAF230, big, polynuclear neutrophilic leukocyte, d230, Single-Cell RNAseq, Sc RNAseq, Procedures, Single Cell Gene Expression Profiling, number, Gene, dTAFII250, broad, EfW1, froggy, Gyltl1a, method, large, Structural, single-cell transcriptome sequencing, dmTAF1, Taf230, Messenger, method used in an experiment, Functional, Studies, Whole Transcriptome Shotgun Sequencing, Low, Technique, TAF250, Taf200, proportion, dTAF[[II]]250, Genetic, cell, Accountings, MDDGB6, neutrophil leucocyte, study., messenger RNA, Taf1p, Single Cell RNAseq, LARGE, Single Cell RNA Seq, Transcriptome Analysis, RNA Seq, neutrophilic leukocyte, L-CA, Sequencing, ScRNA-seq, Study, dTAF250, BPFD#36, template RNA, RNA Sequence Analyses, leukocyte common antigen, GP180, great, RNA Sequencing, PTPRC, RNA-Seq, TAF, 10X sequencing, Sequence Analyses, Leukocyte common antigen, RNA, data, TAF[[II]]250, Single-Cell RNA-Seq, cou, RNA Sequence Determinations, Messenger RNA, l(3)84Ab, BG:DS00004.13, Single Cell Gene Expression Analysis, Cistrons, Cell, Single Cell Transcriptome Analysis, dTAF230, Sc-RNAseq, Lr, LCA, p230, Poly(A)+ mRNA, chemical analysis, TAF[[II]]250/230, INSDC_feature:mRNA, TFIID, rare (European definition), Polyadenylated RNA, Taf[[II]]250, Single-Cell Transcriptome Analyses, Poly(A)+ RNA, TAF[[II]]230, ly-5, mRNA, Poly(A) Tail, Non-Polyadenylated, TAF[II]250, Transcriptome Analyses, Noises, plan specification, chromium, Single-Cell Transcriptome, DmelCG17603, RNA Sequence Analysis, cardinality, Bra, quotient, PMN, polymorphonuclear leucocyte, Structural Genomics, assay, Chromium, poly, Polyadenylated mRNA, polymorphonuclear neutrophil, Severe, TAF1"],"name_synonyms":["Vasp, VASP, DmelCG15112, ENHANCER OF ATNSI ACTIVITY, Data Set, MENA, 116., NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-BIOPIC-21-10-2019-15:54:13:965-116 - samples","description":"Single cell RNA sequencing (scRNA-seq) is widely used for profiling transcriptomes of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently-used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data by the two platforms from the same samples of CD45- cells, we systematically evaluated their features using a wide spectrum of analysis. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data better. For 10X-based data, we observed higher noise for mRNA in the low expression level. Despite the poly(A) enrichment, approximately 10-30% of all detected transcripts by both platforms were from non-coding genes, with lncRNA accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can better detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected different sets of differentially expressed genes between cell clusters, indicating the complementary nature of these technologies. Our comprehensive benchmark analysis offers the basis for selecting the optimal scRNA-seq strategy based on the objectives of each study.","dates":{"updated":"2019-10-22 11:54:00"},"accession":"EGAD00001005448","cross_references":{"TAXONOMY":["9606"],"EGA":["EGAC00001000551","EGAS00001003973"]}}