run_metadata: 40743
This data as json
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| 40743 | SRR3342393 | SRX1684659 | SRS1379870 | SRP072957 | PRJNA317597 | FOXN3 regulates hepatic glucose utilization | GSE80003 | Transcriptome Analysis | We sequenced mRNA from livers of 7 dpf transgenic zebrafish overexpressing foxn3 in the liver and non transgenic siblings Overall design: Examination of the changes in level of different mRNAs in foxn3 transgenic and wild type siblings | pubmed:27292639 | Transgenic3 | GSM2109873 | source name:foxn3 overexpression liver|tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae | Transgenic3 | Reads were aligned to the genome using novoalign Annotated splice junctions generated by the MakeTranscriptome command in the USeq Splice junction reads were then converted to genomic coordinates using the SamTranscriptomeParser command in USeq Differential gene expression analysis was performed on the resulting count table using DESeq2 Genome build: Zv9 genome build Supplementary files format and content: excel file with read counts FPKM and statistical analysis | foxn3 overexpression liver | Total RNA extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine | tissue:Liver|transgene:foxn3|developmental stage:7 dpf larvae | GSM2109873 | GSM2109873: Transgenic3; Danio rerio; RNA Seq | GSM2109873 | 1 | Total RNA extracted using a DirectZol RNA miniprep kit Zymo Research Illumina TruSeq Stranded Total RNA Sample Prep Kit was used to prepare the library; Samples were barcoded as Transgenic versus wild type and single end 50 bp reads were generated on a Hiseq 2500 machine | GEO Accession:GSM2109873 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP072957 | 11405X8_150225_D00294_0165_AC6BKMANXX_7.txt.gz | fastq | 1538486450.0 | 30769729.0 | GSM2109873 r1 | 0:50 | A:399631224;C:339577730;G:345815787;T:453436273;N:25436 | 50 | 399631224 | 339577730 | 345815787 | 453436273 | 25436 | SRX1684659 | SRS1379870 | SRA405566 | GEO | Amnon Schlegel, Molecular Medicine Program, University of Utah School of Medicine | 1 | 0.89036 | 0.28368 | 0.75461 | 0.63309 | 50 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-04-06 | Larval | Larval | Liver | Liver and Biliary System |