run_metadata: 36334
This data as json
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| 36334 | SRR398323 | SRX115581 | SRS285698 | SRP010291 | PRJNA150927 | miR 221 is required for endothelial tip cell behaviors during vascular development | GSE35078 | Transcriptome Analysis | Through deep sequencing and functional screening in zebrafish we find that miR 221 is essential for angiogenesis. miR 221 knockdown phenocopied defects associated with loss of the tip cell expressed Flt4 receptor. Furthermore miR 221 was required for tip cell proliferation and migration as well as tip cell potential in mosaic blood vessels. miR 221 knockdown also prevented “hyper angiogenesis” defects associated with Notch deficiency and miR 221 expression was inhibited by Notch signaling. Finally miR 221 promoted tip cell behavior through repression of two targets: cyclin dependent kinase inhibitor 1b cdkn1b and phosphoinositide 3 kinase regulatory subunit 1 pik3r1. These results identify miR 221 as an important regulatory node through which tip cell migration and proliferation are controlled during angiogenesis. Overall design: Identification of endothelial expressed microRNA from FACS isolated zebrafish endothelial cells. | pubmed:22340502 | kdrl:egfp pos microRNA | GSM861785 | tissue:FACS isolated kdrl:egfp positive cells|genotype:Tgkdrl:egfp|age:24 hpf|development stage:embryo|cell type:endothelial cells | kdrl:egfp pos microRNA | The standard Illumina pipeline was applied for base calls and quality scoring; sequence tags were subsequently analyzed using miR Deep2. | FACS isolated kdrl:egfp positive cells | Tgkdrl:egfp embryos were dissociated at 24 hpf followed by fluorescence activated cell sorting to isolate GFP positive and negative cells. | Small RNAs were isolated by polyacrylamide gel electrophoresis and ligated to RNA adapters followed by cDNA synthesis and amplification with Illumina primers. | genotype:Tgkdrl:egfp|age:24 hpf|developmental stage:embryo|cell type:endothelial cells | GSM861785 | GSM861785: kdrl:egfp pos microRNA; Danio rerio; RNA Seq | GSM861785 1 | GSM861785: kdrl:egfp pos microRNA | 1 | GEO Accession:GSM861785 | RNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina Genome Analyzer | <SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>36</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR> | SRP010291 | miRNA_GFP_PLUS.fastq.gz | fastq | 265629096.0 | 7378586.0 | GSM861785 r1 | 0:36 | A:67563811;C:62134550;G:62283750;T:67966396;N:5680589 | 36 | 67563811 | 62134550 | 62283750 | 67966396 | 5680589 | SRX115581 | SRS285698 | SRA049243 | GEO | Nathan Lawson Lab, PGFE, Umass Medical School | 1 | 0.01356 | 0.01279 | 0.99924 | 0.3125 | 36 | B | usable mapping rate | illumina | early_illumina | unknown | size_fractionation | unknown | bulk | unknown | unknown | United States | 2012-01-12 | Pharyngula | Embryo | Embryo Imprecise | All anatomical structures |