run_metadata: 40347
This data as json
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| 40347 | SRR3086887 | SRX1518386 | SRS1236745 | SRP068114 | PRJNA307985 | Transcription profiling of zebrafish fin regeneration | GSE76564 | Transcriptome Analysis | We compared transcriptional profiles of regenerating zebrafish caudal fins following fin amputation with profiles from uninjured zebrafish caudal fins Overall design: Examination of whole fin transcriptional profiles from regenerating fins 2 pools of 10 fins and uninjured fins 2 pools of 10 fins | pubmed:27049946 | ZF 4dpa Fin 1 | GSM2028017 | tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation | ZF 4dpa Fin 1 | Base calling with Casava Alignment with TopHat Counts summarized with R using TopHat output Analysis performed with EdgeR package of Bioconductor Genome build: Zv9 Supplementary files format and content: "Regenerate fin counts.txt" and "Uninjured fin Control counts.txt" is a tab delimited text file containing summarized counts for each transcript. This was the dataset entered into edgeR. | Fins 4d post amputation | Fins were amputated to 50% of their original length using razor blades | Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries | strain:EK|line:Wild type|treatment:Fin Amputation | GSM2028017 | GSM2028017: ZF 4dpa Fin 1; Danio rerio; RNA Seq | GSM2028017 | 1 | Either uninjured fins or fins at 4 dy post amputation were collected. 10 fins were dissected rinsed in PBS placed in Trizol and homogenized. RNA was then extracted. Illumina RNA Seq 50 bp Single end libraries | GEO Accession:GSM2028017 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer II | SRP068114 | Reg1-4.fastq.gz | fastq | 90897750.0 | 1817955.0 | GSM2028017 r4 | 0:50 | A:23579811;C:21833091;G:21640955;T:23843357;N:536 | 50 | 23579811 | 21833091 | 21640955 | 23843357 | 536 | SRX1518386 | SRS1236745 | SRA329570 | GEO | Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center | 1 | 0.91241 | 0.06085 | 0.7152 | 0.46013 | 50 | B | usable mapping rate | illumina | early_illumina | full_length | random_priming | unknown | bulk | unknown | unknown | United States | 2016-01-05 | Undetermined | Undetermined | Fin | Surface Structure |