run_metadata: 47605
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 47605 | SRR6661135 | SRX3638231 | SRS2904482 | SRP131956 | PRJNA432507 | Hrg1 promotes heme iron recycling during erythrophagocytosis in zebrafish kidne | GSE109978 | Transcriptome Analysis | RNA seq datasets on adult zebrafish kidneys and spleens non PHZ phenylhydrazine and PHZ treated to compare the gene expression on Tü wild type and hrg1 knockout zebrafish. Overall design: The kidney and Spleen from 5 mpf 6 mpf adult zebrafish Tü hrg1 doulble knockout DKO both non PHZ and PHZ treated were dissected out and flash frozen in TRIzol for RNA extraction. Total of 24 samples with single end 50 base reads were sequenced with HiSeq 2500 Illumina; with triplicate libraries of spleens and kidneys. | pubmed:30248094 | KidDKO 2 | GSM2975179 | source name:whole animal|tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO | KidDKO 2 | Bcl2fastq v2.18 was used to convert the bcl files to fastq files. We aligned to GRCz10 reference genome using STAR version 2.5.2b. We counted number of reads mapped to genes using htseq version 0.6.1p1. Differential gene expression analysis was performed using DESeq2 version 1.12.3 with the cutoff of 0.05 on False Discovery Rate FDR. R version 3.3.2 2016 10 31 was used and Bioconductor version 3.4 with BiocInstaller version 1.24.0 were used. For gene annotation we used Ensembl GRCz10 release 87. | whole animal | Adult zebrafish are treated in Phenylhydrazine containg 2.5 µg/ml fish water | TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation | Normal zebrafish husbandary | tissue:kidney|age:5 mpf 6 mpf|genotype:Tu/hrg1 doulble knockout DKO | GSM2975179 | GSM2975179: KidDKO 2; Danio rerio; RNA Seq | GSM2975179 | 1 | TRIzol + Qiagen miniRNA clean up NEBnext Ultra RNA prep with magnetic mRNA isolation | GEO Accession:GSM2975179 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP131956 | KidDKO_2.fastq.gz | fastq | 720757194.0 | 14132494.0 | GSM2975179 r1 | 0:51 | A:198433339;C:163064446;G:163967236;T:195280391;N:11782 | 51 | 198433339 | 163064446 | 163967236 | 195280391 | 11782 | SRX3638231 | SRS2904482 | SRA654641 | GEO | Laboratory of Molecular Biology, NIH/NIDDK | 1 | 0.92921 | 0.11261 | 0.7063 | 0.52644 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | nebnext | bulk | unknown | unknown | United States | 2018-02-01 | Adult | Adult | Kidney | Renal System |