run_metadata: 71339
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 71339 | SRR21497247 | SRX17500543 | SRS15052259 | SRP396406 | PRJNA878705 | Effect of chronic stress on zebrafish testicular gene expression | GSE212999 | Transcriptome Analysis | To investigate the potential deleterious impact of chronic stress at molecular level in testicular tissue we exposed zebrafish males to chronic stress during 21 days covering around three complete cycles of spermatogenesis in the species Overall design: We then performed gene expression profiling in the stress exposed group and the control one. | Sample 3 AU1008 CTRL3 | GSM6568310 | source name:Testicle|tissue:Testicle|genotype:WT|treatment:Control | Sample 3 AU1008 CTRL3 | Alignment using STAR 2.7.8a using ENCODE parameters Quantification using RSEM 1.3.0 Quantification with annotation Ensembl release 104 Assembly: GRCz11 Supplementary files format and content: TSV file with raw counts | Testicle | RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis. | tissue:Testicle|genotype:WT|treatment:Control | GSM6568310 | GSM6568310: Sample 3 AU1008 CTRL3; Danio rerio; RNA Seq | GSM6568310 r1 | GSM6568310 | 1 | RNA was harvested using with Qiazol; a miRNeasy tissue kit Qiagen. Only samples meeting the requirements 3 µg of RNA; RNA integrity number RIN > 8 were used in RNA seq analysis. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP396406 | loader:fastq load.py | AU1008_6479AF_HFYVNDRXY_2_12UDI-idt-UMI_1.fastq.gz AU1008_6479AF_HFYVNDRXY_2_12UDI-idt-UMI_2.fastq.gz | fastq fastq | 5986839714.0 | 58694507.0 | GSM6568310 r2 | 0:51 1:51 | A:1376941205;C:1669376884;G:1591045173;T:1349265748;N:210704 | 51 | 51 | 1376941205 | 1669376884 | 1591045173 | 1349265748 | 210704 | SRX17500543 | SRS15052259 | SRA1494713 | CNAG | REPROMOL, Molecular Biology, Universidad de León | 2 | 0.96969 | 0.9685 | 0.32009 | 0.32581 | 0.7849 | 0.7876 | 0.71867 | 0.72919 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Spain | 2022-09-09 | Undetermined | Undetermined | Gonad | Reproductive System |