run_metadata: 40340
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 40340 | SRR3086888 | SRX1518387 | SRS1236747 | 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 2 | GSM2028018 | tissue:Fins 4d post amputation|strain:EK|line:Wild type|treatment:Fin Amputation | ZF 4dpa Fin 2 | 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 | GSM2028018 | GSM2028018: ZF 4dpa Fin 2; Danio rerio; RNA Seq | GSM2028018 | 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:GSM2028018 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer II | SRP068114 | Reg2-1.fastq.gz | fastq | 800000000.0 | 16000000.0 | GSM2028018 r1 | 0:50 | A:208862526;C:192270727;G:188582591;T:210215639;N:68517 | 50 | 208862526 | 192270727 | 188582591 | 210215639 | 68517 | SRX1518387 | SRS1236747 | SRA329570 | GEO | Kenneth Poss lab, Department of Cell Biology, Duke University Medical Center | 1 | 0.92514 | 0.07091 | 0.70638 | 0.46239 | 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 |