run_metadata: 48102
This data as json
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|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 48102 | SRR7041784 | SRX3973822 | SRS3199282 | SRP141198 | PRJNA451019 | Potential role of gas6 in zebrafish hindbrain development | GSE113396 | Transcriptome Analysis | identification of differentially expressed genes in gas6 homozygous mutant hindbrain when compared to wildtype hindbrain in zebrafish Overall design: Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer. | parent bioproject:PRJNA451178 | pubmed:29945667 | wildtype control replicate 1 gas6mut | GSM3105070 | source name:dissected hindbrain|developmental stage:48 hpf control|tissue:hindbrain | wildtype control replicate 1 gas6mut | reads quality check with FastQC alignment and read counts with RSEM v1.2.28 Normalized abundance measurements and identification of differentially expressed genes with DESeq2 Genome build: GRCz10/DanRer7 Supplementary files format and content: .tsv containing read count tmp values from each replicate adjusted p values and fold change compared to wildtype samples for all genes detected | dissected hindbrain | Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer. | zebrafish egg water maintained at 28°C | developmental stage:48 hpf control|tissue:hindbrain | GSM3105070 | GSM3105070: wildtype control replicate 1 gas6mut; Danio rerio; RNA Seq | GSM3105070 | 1 | Total RNA was extracted from dissected hindbrain of gas6 homzygous mutants and wildtype embryos at 48hpf using the RNeasy Mini Kit Qiagen. Three libraries from wildtype embryos and three libraries from gas6 mutants were then generated from 3mg RNA using the TruSeq Stranded mRNA Library Prep Kit Illumina. All libraries were analyzed for quality on a bioanalyzer prior to sequencing Agilent 2100 BioAnalyzer. | GEO Accession:GSM3105070 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 2000 | SRP141198 | WT1.fastq.gz | fastq | 3390648900.0 | 33906489.0 | GSM3105070 r1 | 0:100 | A:815584808;C:833592815;G:824903141;T:913622836;N:2945300 | 100 | 815584808 | 833592815 | 824903141 | 913622836 | 2945300 | SRX3973822 | SRS3199282 | SRA693051 | GEO | Biochemistry and Molecular Pharmacology, UMass Medical School | 1 | 0.96267 | 0.05448 | 0.69798 | 0.46774 | 100 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2018-04-19 | Hatching | Embryo | Brain | Nervous System |