run_metadata: 72722
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 72722 | SRR23093179 | SRX19045596 | SRS16462353 | SRP417750 | PRJNA924320 | 'A CRISPR Cas9 mutation in sox9b long intergenic noncoding RNA slincR affects zebrafish development behavior and regeneration | GSE222975 | Transcriptome Analysis | transcriptomic data for 48 hpf Wildtype slincRosu3 sg6; slincR +18 bp mutant and BigD slincR 131 bp mutant zebrafish embryos developmentally exposed to TCDD. Overall design: Two treatments Controls "0" and 1 ng/mL TCDD "1" exposed from 6 hpf 48 hpf. Embryos collected at 48 hpf and then run through library prep and sequencing on a Beijing Genomics Institute DNBseq 500 platform with 100 bl PE | pubmed:37220911 | BigD 0 Replicate 2 | GSM6936123 | source name:Zebrafish embryonic total RNA|tissue:whole embryos|geo loc name:missing|collection date:missing | BigD 0 Replicate 2 | SOAPnuke for read filter HISAT2 for genome mapping STAR for reference genome map DEseq2 for differential expression Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: .xlsx with read counts filtered files and gene expression for all samples. | Zebrafish embryonic total RNA | none provided | tissue:whole embryos | GSM6936123 | GSM6936123: BigD 0 Replicate 2; Danio rerio; RNA Seq | GSM6936123 r1 | GSM6936123 | 1 | none provided | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | DNBSEQ | DNBSEQ-G50 | SRP417750 | BigD-0-2_1.fq BigD-0-2_2.fq | fastq fastq | 4775453400.0 | 47754534.0 | GSM6936123 r1 | 0:100 1:100 | A:1248380099;C:1123077801;G:1142524298;T:1261471202;N:0 | 100 | 100 | 1248380099 | 1123077801 | 1142524298 | 1261471202 | 0 | SRX19045596 | SRS16462353 | SRA1575131 | SARL, Environmental Molecular Toxicology, Oregon State University | SARL, Environmental Molecular Toxicology, Oregon State University | 1 | 0.94724 | 0.0772 | 0.69723 | 0.47889 | 100 | B | usable mapping rate | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2023-01-16 | Undetermined | Embryo | Whole Organism | All anatomical structures |