run_metadata: 40358
This data as json
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| 40358 | SRR3109808 | SRX1538262 | SRS1254844 | SRP068656 | PRJNA309293 | RNA sequencing of adult zebrafish spinal cord | GSE77025 | Transcriptome Analysis | The goal of this study is to determine gene expression changes in the adult zebrafish spinal cord at 2 weeks post complete transection. Overall design: 2 samples were analyzed in duplicates: sham injured spinal cord and transected spinal cord at 2 xxx post injury | pubmed:27811277 | sham spinal cord b | GSM2042682 | source name:spinal cord sham control 2 wks post sham|age:6 month|tissue:spinal cord|tratment:2 wks post sham injury | sham spinal cord b | Quality QC using Fastx Trimming of adapters and short sequences using Fastx Mapping using Bowtie2 Assembly using Cufflinks Quantification using Cuffdiff Genome build: zebrafish Zv9 genome Supplementary files format and content: gene exp.diff file includes gene expression data of injured spinal cord tissue relative to sham injured control tissue | spinal cord sham control 2 wks post sham | Animals underwent complete cervical spinal cord transection and spinal cord tissue was collected 2 xxx post injury. Control animals were sham injured and spinal cord was collected at 2 wks post sham. | RNA was extracted with Trizol reagent followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions | Adult 6 mpf wild type zebrafish were used for this study | age:6 month|tissue:spinal cord|tratment:2 wks post sham injury | GSM2042682 | GSM2042682: sham spinal cord b; Danio rerio; RNA Seq | GSM2042682 | 1 | RNA was extracted with Trizol reagent followed by clean up and DNase I treatment with QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with Agilent Bioanalyser. TruSeq libraries were constructed according to manufacturer's instructions | GEO Accession:GSM2042682 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP068656 | Sample_mm2b.bam | bam | 976598317.0 | 19979953.0 | GSM2042682 r1 | 0:48.88 | A:269123614;C:222873099;G:208746430;T:275819417;N:35757 | 48 | 269123614 | 222873099 | 208746430 | 275819417 | 35757 | SRX1538262 | SRS1254844 | SRA336740 | GEO | Ken Poss Lab, Cell Biology, Duke University Medical Center | 1 | 0.95785 | 0.09352 | 0.71433 | 0.48637 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-01-20 | Adult | Adult | Spinal Cord | Nervous System |