Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Single-cell RNA sequencing data of zebrafish lymphatic and venous endothelial cells at different developmental stages (36 hpf, 48 hpf, 120 hpf (5 dpf) and 168 hpf (7 dpf))

ABSTRACT: This dataset contains single-cell RNA sequencing (scRNA-seq) profiles of zebrafish venous and lymphatic endothelial cells across development. Endothelial cells were isolated by FACS from transgenic zebrafish embryos and larvae at 36 hpf, 48 hpf, 5 dpf (120 hpf), and 7 dpf (168 hpf) using endothelial reporters labeling fli1a-positive and lyve1b-positive endothelial populations, enriching for venous endothelial cells (VECs) and lymphatic endothelial cells (LECs). Transcriptomes were generated using Smart-Seq2. The dataset captures transcriptional heterogeneity across endothelial populations and developmental stages, including proliferating, differentiating, and mature LEC and VEC states during vascular development. These data were used in two studies. In Gloger et al., the dataset was used to identify transcriptional programs regulating spatio-temporal lymphatic endothelial cell proliferation, revealing a lineage-enriched LEC proliferation signature. In Panara, Arnold, Gloger et al., the scRNA-seq data were integrated with ATAC-seq and Hi-C datasets to define regulatory programs and chromatin organisation underlying lymphatic endothelial cell differentiation and gene regulation.

INSTRUMENT(S): Aria III (BD Biosciences), oligo(dT) primer and SuperScript II reverse transcriptase (ThermoFisher Scientific), TapeStation 4200 or 2100 Bioanalyzer with a DNA High Sensitivity chip (Agilent Biotechnologies), STAR v2.5.3a, rpkmforgenes, RSeQC 2.6.1, Illumina Nextera XT index kits (Set A–D), Illumina HiSeq 3000

ORGANISM(S): Danio rerio

SUBMITTER: Katarzyna Koltowska

PROVIDER: E-MTAB-16797 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:We use the zebrafish embryo model to study the similarities and differences in the innate immune response against three different bacterial pathogens. Therefore, we injected E. tarda, Salmonella, or M. marinum into the caudal vein of 28 hours post fertilization (hpf) zebrafish embryos and analysed their gene expression profile at 8 hours or 4 days after infection by microarrays. The results show that infections with the gram-negative bacteria E. tarda and S. typhimurium, which are lethal within 1-2 days, induce a strong early immune response at 8 hours after infection. In contrast, infection with M. marinum leads to a chronic infection that only induces a strong response at 4 days post infection. This microarray study was designed to determine the gene expression profile during infection with Salmonella typhimurium, Mycobacterium marinum, and Edwardsiella tarda. RNA was isolated from single embryos and each treatment group consisted of three embryos: (1) Wildtypes injected with PBS 8 hours post infection (hpi), (2) S. typhimurium-infected wildtypes 8hpi, (3) wildtypes injected with PBS/2%PVP 8hpi , (4) M. marinum-infected wildtypes 8hpi, (5) wildtypes injected with PBS/2%PVP 4 days post infection (dpi), (6) M. marinum-infected wildtypes 4dpi, (7) wildtypes injected with PBS 8hpi (E. tarda control), (8) E. tarda-infected wildtypes 8hpi. Embryos were grown at 28.5M-bM-^@M-^S30M-BM-0C in egg water and manually dechorionated at 24 hours post fertilization (hpf). Subsequently, embryos were infected at 28 hpf by micro-injecting 200 colony forming units (CFU) of S. typhimurium SL1027, E. tarda or Mycobacteria marinum M20 bacteria into the caudal vein, or were mock-injected with buffer as a control. After injections embryos were transferred into fresh egg water and incubated for 8 h or 4 days at 28M-BM-0C. After the incubation period, single embryos were snap-frozen in liquid nitrogen and RNA was isolated for microarray analysis. All treatment groups were analyzed using a common reference approach.

Dataset Information

Single-cell RNA sequencing data of zebrafish lymphatic and venous endothelial cells at different developmental stages (36 hpf, 48 hpf, 120 hpf (5 dpf) and 168 hpf (7 dpf))

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