run_metadata: 53495
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 53495 | SRR9886611 | SRX6639067 | SRS5209782 | SRP217245 | PRJNA558074 | Transcriptomic analysis of dj 1 / zebrafish brains compared to wild type siblings | GSE135271 | Transcriptome Analysis | RNA Seq comparing transcript expression in the brains of 3 dj 1 / mutant zebrafish and 3 wild type siblings at 16 wpf Overall design: Brain mRNA profiles of 16 wpf wild type and park7dj 1 / zebrafish were generated by deep sequencing in triplicate using Illumina HiSeq 3000 | pubmed:32859696 | GH6 | GSM4002525 | source name:Brain|strain:LWT|tissue:Brain|age:12 wpf dj 1 / | GH6 | A quality check was carried out using FastQC to make sure there were enough high quality reads. The adaptor sequences were trimmed with cutadapt 1.16 Salmon 0.10.2 was used for pseudo alignment of reads to the transcriptome. Sleuth 0.30.0 was used to test for differential expression. Genome build: GRCZ11 Supplementary files format and content: tab delimited text file including RPKM values for each transcript hypertext markup language document including read counts per sample | Brain | Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. | strain:LWT|tissue:Brain|age:12 wpf dj 1 / | GSM4002525 | GSM4002525: GH6; Danio rerio; RNA Seq | GSM4002525 | 1 | Brains were removed flash frozen in liquid nitrogen and RNA was harvested using Trizol reagent. Zymo RNA Clean & Concentrator 5 kit Cat No. R1013 was used to clean up the total RNA. RNA libraries were prepared for sequencing using 0.5ug of RNA and the NEBNext® PolyA mRNA Magnetic Isolation Module following manufacturers instructions. | GEO Accession:GSM4002525 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 3000 | SRP217245 | GH6_S41_L004_R1_001.fastq-004.gz GH6_S41_L004_R2_001.fastq-009.gz | fastq fastq | 16197223984.0 | 53633192.0 | GSM4002525 r1 | 0:151 1:151 | A:4524520245;C:3580881754;G:3728671047;T:4362276906;N:874032 | 151 | 151 | 4524520245 | 3580881754 | 3728671047 | 4362276906 | 874032 | SRX6639067 | SRS5209782 | SRA931013 | GEO | Biology, University of York | 2 | 0.91745 | 0.9163 | 0.15171 | 0.14974 | 0.69826 | 0.70161 | 0.49509 | 0.48979 | 151 | 151 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | bulk | bulk | bulk | United Kingdom | 2019-08-01 | Juvenile | Juvenile | Brain | Nervous System |