run_metadata: 70206
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 70206 | SRR19572324 | SRX15624358 | SRS13324587 | 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 | 5 NGS2016020501P116 | GSM6215363 | source name:Danio Rerio caudal fin regenerated tissue Control|tissue:caudal fin regenerated tissue|treatment:Control | 5 NGS2016020501P116 | 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 Control | 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:Control | GSM6215363 | GSM6215363: 5 NGS2016020501P116; Danio rerio; RNA Seq | GSM6215363 r1 | GSM6215363 | 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 | 5-NGS2016020501P116_R1.fastq.gz 5-NGS2016020501P116_R2.fastq.gz | fastq fastq | 4168972133.0 | 20866510.0 | GSM6215363 r1 | 0:99.68 1:100.11 | A:1111900344;C:972434705;G:950907789;T:1133536284;N:193011 | 99 | 100 | 1111900344 | 972434705 | 950907789 | 1133536284 | 193011 | SRX15624358 | SRS13324587 | SRA1433229 | NGS, STAB VIDA | NGS, STAB VIDA | 2 | 0.94915 | 0.95043 | 0.08765 | 0.08617 | 0.71167 | 0.71715 | 0.46955 | 0.46253 | 100 | 100 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Portugal | 2022-06-07 | Undetermined | Undetermined | Fin | Surface Structure |