run_metadata: 51073
This data as json
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| 51073 | SRR8503425 | SRX5307302 | SRS4304842 | SRP182846 | PRJNA517717 | Transpositional scaling and niche transitions restore organ size and shape during zebrafish fin regeneration | GSE125859 | Transcriptome Analysis | Regenerating zebrafish fins have distal progenitor and proximal re differentiation zones. A Wnt producing "niche" population maintains distal cells in progenitor states. We sought to define molecular markers of niche cells to study their origins and fates and how they contribute to fin size and shape restoration. Overall design: We used RNA Seq to compare gene expression between three replicates of microdissected distal vs. proximal regenerating fin tissue as distinguished by distal shha:gfp expression. Each replicate consisted of pooled tissue from four caudal fins. | prox 3 | GSM3583369 | source name:96 hpa proximal regenerate|transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation | prox 3 | Basecalling by Illumina Real Time Analysis 2 RTA2. Sequence reads were mapped to GRCz11/danRer11 using TopHat2 Mapped reads were counted using HTSeq Genome build: GRCz11/danRer11 Supplementary files format and content: Tab delimited text files of HTSeq counts for each sample are provided | 96 hpa proximal regenerate | Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. | transgene:shha:eGFP|tissue:regenerating caudal fin|time:96 hours post amputation | GSM3583369 | GSM3583369: prox 3; Danio rerio; RNA Seq | GSM3583369 | 1 | Tissue was collected and immediately placed in TRIzol reagent and homogenized. RNA was isolated using manufacturer's instruction. Libraries were prepared from 1ug of isolated RNA using Kapa stranded mRNA Seq kit and protocol. | GEO Accession:GSM3583369 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP182846 | P_H3_S6_R1_001.fastq | fastq | 2572355378.0 | 30989968.0 | GSM3583369 r1 | 0:83.01 1:0 | A:628074006;C:625169881;G:585755261;T:732650748;N:705482 | 83 | 0 | 628074006 | 625169881 | 585755261 | 732650748 | 705482 | SRX5307302 | SRS4304842 | SRA841050 | GEO | Stankunas, Biology- Institute of Molecular Biology, University of Oregon | 1 | 0.95739 | 0.12653 | 0.72066 | 0.49327 | 84 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2019-01-29 | Undetermined | Undetermined | Fin | Surface Structure |