run_metadata: 49195
This data as json
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| 49195 | SRR7789506 | SRX4644362 | SRS3742432 | SRP159668 | PRJNA489469 | The Lysosomal Transcription Factor TFEB regulates myelination downstream of the Rag Ragulator complex. | GSE119332 | Transcriptome Analysis | Purpose: To identify genes that are differentially expressed in oligodendrocytes between control and rraga mutant zebrafish we performed RNA seq using the Illumina platform Overall design: Oligodendrocytes were isolated from control and rraga mutant zebrafish at 5 dpf using FACS sorting of Cldnk:GFP positive cells. RNA was extracted from these cells and sequenced using standard Illumina protocol. | pubmed:30399334 | Cldnk GFP WT | GSM3370087 | tissue:Oligodendrocytes|strain:TL Tupfel long fin|developmental stage:5 dpf type | Cldnk GFP WT | Trimmed paired end reads from each sample were mapped to zebrafish reference genome using CLC Genomics Workbench 11.0 Danio rerio reference genome and transcriptome was downloaded from CLC Genomics workbench 11.0 Differential expression analysis was performed by comparing mapped control and rraga mutant reads using CLC Genomics Workbench 11.0 while controling for two independent experiments Gene ontology was performed using zebrafish annotations file v1.4 downloaded from Gene Ontology Consortium Genome build: GRCz11 Supplementary files format and content: Fold change | Oligodendrocytes | Cldnk:GFP cells were isolated from wildtype and rraga mutant samples by FACS sorting. Libraries were prepared using Illumina NextSeq Mid | strain:TL Tupfel long fin|developmental stage:5 dpf type | GSM3370087 | GSM3370087: Cldnk GFP WT; Danio rerio; RNA Seq | GSM3370087 | 1 | Cldnk:GFP cells were isolated from wildtype and rraga mutant samples by FACS sorting. Libraries were prepared using Illumina NextSeq Mid | GEO Accession:GSM3370087 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP159668 | cldnkGFP_WT2.fastq.gz cldnkGFP_WT1.fastq.gz | fastq fastq | 6674339658.0 | 46733475.0 | GSM3370087 r1 | 0:71.27 1:71.55 | A:1817040601;C:1501041809;G:1524935125;T:1827161188;N:4160935 | 71 | 71 | 1817040601 | 1501041809 | 1524935125 | 1827161188 | 4160935 | SRX4644362 | SRS3742432 | SRA767417 | GEO | Talbot, Developmental Biology, Stanford University | 2 | 0.93563 | 0.93694 | 0.0541 | 0.05296 | 0.81339 | 0.82572 | 0.52248 | 0.52293 | 76 | 76 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2018-08-31 | Larval | Larval | Fin | Surface Structure |