run_metadata: 66799
This data as json
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| 66799 | SRR16604666 | SRX12805804 | SRS10751265 | 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 36hpa control 2 | GSM5660156 | source name:Fin 36hpa control|strain:Ekkwill|genotype:wild type|treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin | Fin 36hpa control 2 | 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 36hpa 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:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin | GSM5660156 | GSM5660156: Fin 36hpa control 2; Danio rerio; RNA Seq | GSM5660156 | 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:GSM5660156 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP343527 | loader:fastq load.py | 36-HET3_S6_L001_R1_001.fastq.gz 36-HET3_S6_L001_R2_001.fastq.gz | fastq fastq | 22566569480.0 | 74723740.0 | GSM5660156 r1 | 0:151 1:151 | A:5767936654;C:5525950628;G:5631828938;T:5640587381;N:265879 | 151 | 151 | 5767936654 | 5525950628 | 5631828938 | 5640587381 | 265879 | SRX12805804 | SRS10751265 | SRA1318866 | GEO | Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison | 2 | 0.9628 | 0.96333 | 0.04371 | 0.0431 | 0.72914 | 0.7292 | 0.46321 | 0.46573 | 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 |