run_metadata: 70207
This data as json
| rowid | run.accession | experiment.accession | sample.accession | study.accession | bioproject | study.title | study.alias | study.type | study.abstract | study.attributes | study.PMIDs | sample.description | sample.title | sample.alias | sample.centername | sample.attributes | GEOsample.title | GEOsample.dataprocessing | GEOsample.source | GEOsample.treatmentprotocol | GEOsample.extractprotocol | GEOsample.growthprotocol | GEOsample.characteristics | GEOsample.accession | experiment.title | experiment.alias | experiment.library_name | experiment.design_description | experiment.library_construction_protocol | experiment.attributes | experiment.library_strategy | experiment.library_source | experiment.library_selection | experiment.library_layout | experiment.platform | experiment.instrument_model | experiment.spot_descriptor | experiment.study_ref | run.title | run.attributes | run.filename | run.semantic_name | run.total_bases | run.total_spots | run.alias | run.read_lengths | run.base_counts | run.r1_length | run.r2_length | run.r3_length | run.r4_length | run.Acount | run.Ccount | run.Gcount | run.Tcount | run.Ncount | run.experiment | run.pool_member | submission.accession | submission.srasource | submission.bioprojectsource | seqdetective.n_mates | seqdetective.mapping_rate.mate1 | seqdetective.mapping_rate.mate2 | seqdetective.nofeature_rate.mate1 | seqdetective.nofeature_rate.mate2 | seqdetective.sparsity.mate1 | seqdetective.sparsity.mate2 | seqdetective.pos_strand_rate.mate1 | seqdetective.pos_strand_rate.mate2 | seqdetective.readlen.mate1 | seqdetective.readlen.mate2 | seqdetective.judgement.mate1 | seqdetective.judgement.mate2 | seqdetective.judgement.reason | platform_family | instrument_generation | read_bias | selection_class | prep_kit | sc_or_bulk | tech_class | technology | tech_variant | submission.bioprojectsource.country | earliest_date | devstage_curation | devstage_curation_coarse | tissue_curation | tissue_curation_coarse |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 70207 | SRR19572325 | SRX15624357 | SRS13324586 | 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 | 4 NGS2016020501P115 | GSM6215362 | source name:Danio Rerio caudal fin regenerated tissue Control|tissue:caudal fin regenerated tissue|treatment:Control | 4 NGS2016020501P115 | 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 | GSM6215362 | GSM6215362: 4 NGS2016020501P115; Danio rerio; RNA Seq | GSM6215362 r1 | GSM6215362 | 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 | 4-NGS2016020501P115_R1.fastq.gz 4-NGS2016020501P115_R2.fastq.gz | fastq fastq | 5106840970.0 | 25558452.0 | GSM6215362 r1 | 0:99.69 1:100.12 | A:1368703272;C:1185689470;G:1163767029;T:1388450304;N:230895 | 99 | 100 | 1368703272 | 1185689470 | 1163767029 | 1388450304 | 230895 | SRX15624357 | SRS13324586 | SRA1433229 | NGS, STAB VIDA | NGS, STAB VIDA | 2 | 0.94362 | 0.94621 | 0.09241 | 0.09066 | 0.71323 | 0.71482 | 0.47513 | 0.46584 | 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 |