run_metadata: 25153
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 25153 | SRR25649174 | SRX21375287 | SRS18618379 | SRP455253 | PRJNA1005695 | Metagenomic survey of zebrafish from the laboratory and the pet trade | PRJNA1005695 | Other | This study involved sequencing of bulk ribo depleted RNA from intestine kidney and spleen tissues of adult zebrafish reared in the laboratory and the pet trade to identify zebrafish associated microbes in different environments. The goal was to identify viruses and other microbes that infect zebrafish to improve colony health monitoring and highlight pathogens that could be used to study infections of relevance to aquaculture and biomedicine. | 18843X8 | strain:Tubingen|dev stage:adult|collection date:2020 11 05|geo loc name:USA: Salt Lake City UT|sex:male|tissue:kidney|isolation source:lab|replicate:CNTM3|BioSampleModel:Model organism or animal | RNA seq of adult Danio rerio from laboratory and pet trade sources | 18843X8 | 18843X8 | Fish were sacrificed and intestines whole kidney marrows and spleens were harvested for processing. All tissues were homogenized using mechanical lysis. RNA was extracted using the directzol kit Zymo. 1ml of TRIzol was used per intestine and 0.5ml of TRIzol used for individual spleens and kidneys. Following RNA extraction samples were DNAse treated Zymo. RNA ScreenTape Agilent was used to assess quality of RNA samples. Only samples with RIN scores >8 were used for analysis. RNA libraries were prepared by the High Throughput Genomics Shared Resource at the University of Utah with the Illumina TruSeq Stranded Total RNA Library Prep Ribo Zero Gold and sequenced on a Novaseq with using a 150x150 bp sequencing kit to a depth of 25 million reads per sample | RNA-Seq | METATRANSCRIPTOMIC | RANDOM | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP455253 | 18843X8_R1.fastq.gz 18843X8_R2.fastq.gz | fastq fastq | 7615135964.0 | 25215682.0 | 18843X8 R1.fastq.gz | 0:151 1:151 | A:2157897532;C:1663478819;G:1764954395;T:2028683751;N:121467 | 151 | 151 | 2157897532 | 1663478819 | 1764954395 | 2028683751 | 121467 | SRX21375287 | SRS18618379 | SRA1693347 | University of Utah|Quantitative Cell Science | University of Utah | 2 | 0.91455 | 0.91333 | 0.34885 | 0.34782 | 0.69467 | 0.70167 | 0.50339 | 0.51371 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | random_priming | trueseq | bulk | bulk | bulk | United States | 2023-08-15 | Adult | Adult | Kidney | Renal System |