run_metadata: 42113
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 42113 | SRR5418457 | SRX2710003 | SRS2101766 | SRP103090 | PRJNA381761 | A Novel Perivascular Cell Population in the Zebrafish Brain | GSE97421 | Transcriptome Analysis | Purpose: RNA seq analysis from isolated zebrafish fluorescent granular perithelial FGP cells in adult brains compared to endothelial cells or entire fish. Method: FGPs and endothelium were isolated by FACS sorting using transgenic line Tgkdrl:mCherry;Tgmrc1a:eGFP. Overall design: Total RNA from isolated FGPs endothelial cells and whole fish. | pubmed:28395729 | Whole fish | GSM2564303 | source name:Adult fish|strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal | Whole fish | Illumina software for base calling. Reads trimmed using trimmomatc and aligned using RNA STAR. Differential RNA expression was quantified by subread featureCounts and tested by DESeq2. Genome build: Zv10 GRCz10 danRer10 Supplementary files format and content: Raw Counts.txt: Tab delimited text file includes the raw counts of the samples. Supplementary files format and content: GFP RFP.txt: Tab delimited text file includes the comparisons between the GFP+ and mCherry/RFP+ cells. Supplementary files format and content: GFP Whole.txt: Tab delimited text file includes the comparisons between the GFP+ and whole fish cells. | Adult fish | Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols. | strain/background:Ek|genotype/variation:Tgkdrl:mCherry;Tgmrc1a:eGFP|developmental stage:adult|source tissue:Whole animal | GSM2564303 | GSM2564303: Whole fish; Danio rerio; RNA Seq | GSM2564303 | 1 | Manual dissection of whole brain trypsin mechanical dissociation and FACS sorting. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM2564303 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP103090 | fish2_S10Aligned.sortedByCoord.out.bam | bam | 1743231497.0 | 15669069.0 | GSM2564303 r3 | 0:55.66 1:55.60 | A:525584635;C:344650225;G:347621333;T:524323321;N:1051983 | 55 | 55 | 525584635 | 344650225 | 347621333 | 524323321 | 1051983 | SRX2710003 | SRS2101766 | SRA551687 | GEO | Weinstein Lab, NICHD, NIH | 2 | 0.8376 | 0.84959 | 0.44324 | 0.4524 | 0.7585 | 0.77112 | 0.67205 | 0.67177 | 36 | 36 | B | B | biological fallback assumption | illumina | nextseq | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2017-04-05 | Adult | Adult | Whole Organism | All anatomical structures |