run_metadata: 66802
This data as json
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| 66802 | SRR16604663 | SRX12805801 | SRS10751262 | 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 mutant 1 | GSM5660153 | source name:Fin 36hpa mutant|strain:Ekkwill|genotype:scn8abtemca / |treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin | Fin 36hpa mutant 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 36hpa mutant | 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:scn8abtemca / |treatment:Amputated|protocol:33°C for 36 hours|tissue:Regenerating fin | GSM5660153 | GSM5660153: Fin 36hpa mutant 1; Danio rerio; RNA Seq | GSM5660153 | 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:GSM5660153 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP343527 | loader:fastq load.py | 36-MUT2_S7_L001_R1_001.fastq.gz 36-MUT2_S7_L001_R2_001.fastq.gz | fastq fastq | 21653872328.0 | 71701564.0 | GSM5660153 r1 | 0:151 1:151 | A:5580243905;C:5261823509;G:5370184364;T:5441361192;N:259358 | 151 | 151 | 5580243905 | 5261823509 | 5370184364 | 5441361192 | 259358 | SRX12805801 | SRS10751262 | SRA1318866 | GEO | Junsu Kang Lab, Cell and Regenerative Biology, University of Wisconsin-Madison | 2 | 0.96165 | 0.96176 | 0.04508 | 0.04415 | 0.72839 | 0.72894 | 0.4695 | 0.47129 | 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 |