run_metadata: 70209
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 70209 | SRR19572327 | SRX15624355 | SRS13324583 | SRP378897 | PRJNA846701 | Fin ray branching is defined by TRAP+ osteolytic tubules in zebrafish | GSE205599 | Transcriptome Analysis | Study and define how caudal fin rays mineralize and are shaped during regeneration providing a detailed perspective about its formation and bifurcation and identifying key roles of OLTs. Overall design: Comparative gene expression analysis of regenerating zebrafish fins between 1 and 3 dy post amputation | 2 NGS2016020501P113 | GSM6215360 | source name:Danio Rerio caudal fin regenerated tissue 24h|tissue:caudal fin regenerated tissue|treatment:24h | 2 NGS2016020501P113 | CLC Genomics Workbench 9.0.1. Sequence reads were trimmed for adaptor sequence/low quality sequence using CLC genomic benchwork parameter Quality limit: 0.01 Trimmed sequence reads were mapped to GRCz10 using CLC genomic benchwork parameters mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.95 similarity fraction: 0.95 Read count extraction and normalization were performed using CLC genomic benchwork Assembly: GRCz10 Supplementary files format and content: tab delimited text files include RPKM values for each Sample | Danio Rerio caudal fin regenerated tissue 24h | The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi 2006 Illumina TruSeq Stranded mRNA Library Preparation Kit | tissue:caudal fin regenerated tissue|treatment:24h | GSM6215360 | GSM6215360: 2 NGS2016020501P113; Danio rerio; RNA Seq | GSM6215360 r1 | GSM6215360 | 1 | The regenerated tissue was homogenized and a phenolic extraction was performed as previously described in Chomczynski and Sacchi 2006 Illumina TruSeq Stranded mRNA Library Preparation Kit | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP378897 | loader:fastq load.py | 2-NGS2016020501P113_R1.fastq.gz 2-NGS2016020501P113_R2.fastq.gz | fastq fastq | 6010524551.0 | 30053957.0 | GSM6215360 r1 | 0:99.79 1:100.20 | A:1621952736;C:1386940946;G:1353305703;T:1648081487;N:243679 | 99 | 100 | 1621952736 | 1386940946 | 1353305703 | 1648081487 | 243679 | SRX15624355 | SRS13324583 | SRA1433229 | NGS, STAB VIDA | NGS, STAB VIDA | 2 | 0.94314 | 0.94585 | 0.09385 | 0.09216 | 0.72174 | 0.72441 | 0.49514 | 0.48343 | 101 | 101 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Portugal | 2022-06-07 | Undetermined | Undetermined | Fin | Surface Structure |