run_metadata: 48181
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 48181 | SRR7089631 | SRX4018601 | SRS3239988 | SRP144228 | PRJNA454503 | RNA seq of zebrafish ptk7 mutants with mild and severe scoliosis and ptk7+Tgfoxj1a:ptk7 straight siblings | PRJNA454503 | Other | To identify molecular mechanisms underlying scoliosis spine curvature we performed next generation RNA sequencing on ptk7 mutant vs. ptk7+Tgfoxj1a:ptk7 sibling fish at an age correlating with mild scoliosis and severe scoliosis 0.8 cm length. Because the tissue of idiopathic scoliosis origin remains unknown RNA Seq was performed on bulk RNA samples collected from the entire trunk and tail heads were removed at the level of the gill to eliminate signals associated with abnormal Ptk7 function in the brain. | ptk7 + Tgfoxj1a::ptk7 sm 47 | isolate:fish #47|age:21 dpf|sex:NA|tissue:trunk|genotype:ptk7 + Tgfoxj1a::ptk7|BioSampleModel:Model organism or animal | RNA sequencing of Danio rerio: mild and severe scoliosis trunk | tg ptk7 sm 47 | tg ptk7 sm 47 | Total RNA extraction was preformed using the Qiagen RNeasy kit following the manufacturer's instructions Qiagen. RNA sample quality was assessed using an Agilent Bioanalyzer. Library prep and subsequent sequencing was performed by The Centre for Applied Genomics at The Hospital for Sick Children SickKids using the NEBNext stranded RNA | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP144228 | Tg_ptk7_gfp_mut_47_R1.fastq.gz Tg_ptk7_gfp_mut_47_R2.fastq.gz | fastq fastq | 14696368344.0 | 58318922.0 | Tg ptk7 gfp mut 47 R1.fastq.gz | 0:126 1:126 | A:3846748622;C:3493221776;G:3499013500;T:3855890141;N:1494305 | 126 | 126 | 3846748622 | 3493221776 | 3499013500 | 3855890141 | 1494305 | SRX4018601 | SRS3239988 | SRA698292 | The Hospital for Sick Children|Developmental and Stem Cell Biology | The Hospital for Sick Children | 2 | 0.9603 | 0.96246 | 0.04242 | 0.0418 | 0.71309 | 0.71419 | 0.53374 | 0.53777 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | bulk | bulk | bulk | Canada | 2019-11-26 | Larval | Larval | Trunk | Surface Structure |