run_metadata: 40976
This data as json
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| 40976 | SRR3498290 | SRX1756836 | SRS1433367 | SRP074848 | PRJNA321321 | microRNAs Establish and Maintain Uniform Cellular Phenotypes during the Architecture of Complex Tissues | GSE81340 | Transcriptome Analysis | Proper functioning of tissues requires cells to behave in uniform well organized ways. Conversely many diseases involve increased cellular heterogeneity due to genetic and epigenetic alterations. Defining the mechanisms that counteract phenotypic variability is therefore critical to understand how tissues sustain homeostasis. Here we carried out a single cell resolution screen of zebrafish embryonic blood vessels upon mutagenesis of single microRNA miRNA genes and multi gene miRNA families. We found that miRNA mutants exhibit a profound increase in cellular phenotypic variability of specific vascular traits. Genome wide analysis of endothelial miRNA target genes identified antagonistic regulatory nodes of vascular growth and morphogenesis signaling that allow variable cell behaviors when derepressed. Remarkably lack of such miRNA activity greatly sensitized the vascular system to microenvironmental changes induced by pharmacological stress. We uncover a previously unrecognized role of miRNAs as a widespread protective mechanism that limits variability in cellular phenotypes. This discovery marks an important advance in our comprehension of how miRNAs function in the physiology of higher organisms. Overall design: Analysis of differential genes expression in Zebrafish endothelial cells for 4 different developmental stages in duplicate | parent bioproject:PRJNA321317 | pubmed:28350988;pubmed:33273096 | NoEndo 48hpf E1 | GSM2150815 | source name:Endothelial cell|developmental stage:48hpf|tissue:Endothelial|stain:GFP | NoEndo 48hpf E1 | Illumina Casava1.7 software used for basecalling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to Zv9 whole genome using STAR v2.3.0 Fragments Per Kilobase Of Exon Per Million Fragments Mapped FPKM were calculated using Cufflink software Annotation gtf for Zv9 Genome build: Zv9 Supplementary files format and content: tab delimited text files include RPKM values for each Sample ... | Endothelial cell | Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols | Zebrafish embryos were raised according standard protocols at 28˚C and according to protocols approved by Yale University Institutional Animal Care and Use Committee # 2015 11473. | developmental stage:48hpf|tissue:Endothelial|stain:GFP | GSM2150815 | GSM2150815: NoEndo 48hpf E1; Danio rerio; miRNA Seq | GSM2150815 | 1 | Transgenic fish were treated with Liberase to disociate the cells. post FACS sorting the GFP positive cells were lisate and RNA was harvested using Trizol reagent. Illumina TruSeq RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM2150815 | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | SRP074848 | NoEndo_48hpf_E1.fastq.gz | fastq | 1204752152.0 | 15852002.0 | GSM2150815 r1 | 0:76 | A:297517299;C:293969730;G:317491224;T:295696492;N:77407 | 76 | 297517299 | 293969730 | 317491224 | 295696492 | 77407 | SRX1756836 | SRS1433367 | SRA424808 | GEO | Internal Medicine, Yale University | 1 | 0.0 | 0.0 | 1.0 | 76 | T | under 1.2% mapping rate | illumina | early_illumina | unknown | size_fractionation | trueseq | bulk | unknown | unknown | United States | 2016-05-11 | Hatching | Embryo | Endothelium | Cardiovascular System |