run_metadata: 43736
This data as json
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| 43736 | SRR6039682 | SRX3187832 | SRS2515280 | SRP117696 | PRJNA407368 | RNA seq timecourse analysis during zebrafish heart looping morphogenesis | PRJNA407368 | Other | During embryogenesis the heart forms as a linear tube that then undergoes multiple simultaneous morphogenetic events to obtain its mature shape. To understand the gene regulatory networks GRNs driving this phase of heart development during which many congenital heart disease malformations likely arise we conducted an RNA seq timecourse in zebrafish from 30 hpf to 72 hpf and identified 5861 genes with altered expression. We clustered the genes by temporal expression pattern identified transcription factor binding motifs enriched in each cluster and generated a model GRN for the major gene batteries in heart morphogenesis. | A60 | time point hpf group:A|multiplex group:1|strain:cmlc2::gfp reporter line|dev stage:60 hpf organism or animal | RNA Seq of Danio rerio heart tissue: Time series during heart looping 30 72 hpf | A60 | A60 | For each replicate approximately 1600 zebrafish embryos were collected 200 each at 30 36 42 48 54 60 66 72 hpf Hearts were mechanically separated from the embryos and manually pipetted from the media. Isolated hearts were centrifuged briefly and the supernatant removed. 400 ul of Trizol was then added to the pellet and homogenized before storing at 80C. RNA was isolated by phenol chloroform extraction followed by ethanol precipitation. A total of 6 replicate experiments were performed. To ensure sufficient material for library preparation each of the 3 replicate groups was formed by pooling 2 of the 6 experiments. RNA Seq libraries were constructed from total RNA using the NuGEN Ovation RNA Seq System v2 ultra low input kit. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP117696 | 9499X6_130405_SN141_0668_AD2154ACXX_7.txt.gz | fastq | 1644194800.0 | 32883896.0 | 9499X6 130405 SN141 0668 AD2154ACXX 7.txt.gz | 0:50 | A:384925336;C:429204709;G:426105707;T:403838669;N:120379 | 50 | 384925336 | 429204709 | 426105707 | 403838669 | 120379 | SRX3187832 | SRS2515280 | SRA608458 | University of Utah|Neurobiology and Anatomy | University of Utah | 1 | 0.21132 | 0.06222 | 0.92161 | 0.73478 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2017-09-14 | Hatching | Embryo | Heart | Cardiovascular System |