run_metadata: 66796
This data as json
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| 66796 | SRR16604669 | SRX12805807 | SRS10751268 | SRP343527 | PRJNA775662 | Regulation of fin regeneration by a voltage gated sodium channel | GSE186729 | Transcriptome Analysis | We compare the brain and fin RNA seq profiles of wild type and scn8ab mutant zebrafish which exhibit locomotion and fin regeneration defects. Overall design: Biological duplicate brain and fin profiles of adult wild type sibling and scn8abtemca mutant zebrafish. Corresponding sample pools include: whole brain of wild type siblings and temca mutants and uninjured and 36 hpa fins of wild type siblings and temca mutants at the restrictive temperature 33 degrees | Fin uninjured control 1 | GSM5660159 | source name:Fin uninjured control|strain:Ekkwill|genotype:wild type|treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin | Fin uninjured control 1 | Cutadapt to remove adapter sequences and short reads less than 10bp HISAT2 to align to zebrafish GRCz11 reference genome FeatureCount Genome build: GRCz11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample | Fin uninjured control | Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | strain:Ekkwill|genotype:wild type|treatment:Uninjured|protocol:33°C for 36 hours|tissue:Uninjured fin | GSM5660159 | GSM5660159: Fin uninjured control 1; Danio rerio; RNA Seq | GSM5660159 | 1 | Tissues were homogenized in immediately post dissection and RNA was extracted using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | GEO Accession:GSM5660159 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP343527 | loader:fastq load.py | UN-HET2_S1_L001_R2_001.fastq.gz UN-HET2_S1_L001_R1_001.fastq.gz | fastq fastq | 27479475884.0 | 90991642.0 | GSM5660159 r1 | 0:151 1:151 | A:7093156924;C:6670638365;G:6882029592;T:6833331180;N:319823 | 151 | 151 | 7093156924 | 6670638365 | 6882029592 | 6833331180 | 319823 | SRX12805807 | SRS10751268 | SRA1318866 | GEO | Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison | 2 | 0.94831 | 0.83016 | 0.04913 | 0.04202 | 0.74079 | 0.75262 | 0.454 | 0.44756 | 151 | 151 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2021-10-27 | Undetermined | Undetermined | Fin | Surface Structure |