run_metadata: 68481
This data as json
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| 68481 | SRR17818763 | SRX13980636 | SRS11817959 | SRP357386 | PRJNA801875 | YAP regulates an SGK1/mTORC1/SREBP dependent lipogenic program to support proliferation and tissue growth | GSE195711 | Transcriptome Analysis | We report the role of YAP in promoting de novo lipogenesis through the SREBP transcriptional program. By using paired end RNA sequencing we show that transgenic zebrafish livers expressing activted YAP exhibit an increase in SREBP target genes associated with lipogenesis. The paired end RNA sequencing was performed in larval zebrafish livers at 7 dpf 7 dpf Overall design: Examination of differentially expressed genes in larval livers isolated from WT and transgenic lf:YAP zebrafish. | pubmed:35216681 | lfYap 2 S48 R1 001 and lfYap 2 S48 R2 001 | GSM5848712 | tissue:larval zebrafish liver pool of 10|strain:lf:YAP YAP activation specific to hepatocytes | lfYap 2 S48 R1 001 and lfYap 2 S48 R2 001 | Sequencing files were convereted to FastQ files using Galaxy Reads were trimmed using Cutadapt v1.16 Reads were mapped to zebrafish genome Ensembl danrer10 using HISAT v2.1.0 Counting was performed using featurecounts v1.6.0 Differentially expressed genes were identified using Degust Limma Voom v3.40.6 Genome build: Reads were mapped to zebrafish genome Ensembl danrer10 Supplementary files format and content: csv file containing the counts for all samples in the study WT 1 2 3 4 and lf:YAP 1 2 3 4 | larval zebrafish liver pool of 10 | No treatment involved | Larval zebrafish livers were dissected and transferred into TRIzol solution. RNA was extracted using an Direct zol RNA miniPREP kit. RNA quality was confirmed a Tapestation system before sequencing Libraries were prepared in accordance to SMARTer Stranded Total RNA seq Kit V2 Pico Input Libraries were sequeced using an Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M per sample | Zebrafish larvae were raised from 3 7 days in a 6 well plate before liver dissection at 7 dpf | strain:lf:YAP YAP activation specific to hepatocytes | GSM5848712 | GSM5848712: lfYap 2 S48 R1 001 and lfYap 2 S48 R2 001; Danio rerio; RNA Seq | GSM5848712 r1 | GSM5848712 | 1 | Larval zebrafish livers were dissected and transferred into TRIzol solution. RNA was extracted using an Direct zol RNA miniPREP kit. RNA quality was confirmed a Tapestation system before sequencing Libraries were prepared in accordance to SMARTer Stranded Total RNA seq Kit V2 Pico Input Libraries were sequeced using an Illumina NextSeq 500 with paired end 75bp reads to a depth of 15M per sample | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP357386 | loader:fastq load.py | lfYap-2_S48_R1_001.fastq.gz lfYap-2_S48_R2_001.fastq.gz | fastq fastq | 1516250700.0 | 10108338.0 | GSM5848712 r1 | 0:75 1:75 | A:312158916;C:440991780;G:454294642;T:308530769;N:274593 | 75 | 75 | 312158916 | 440991780 | 454294642 | 308530769 | 274593 | SRX13980636 | SRS11817959 | SRA1364100 | PeterMacCallum Cancer Centre | PeterMacCallum Cancer Centre | 2 | 0.9509 | 0.95002 | 0.17901 | 0.18719 | 0.87178 | 0.87399 | 0.74101 | 0.76543 | 75 | 75 | B | B | biological fallback assumption | illumina | nextseq | full_length | cdna_unspecified | smarter | bulk | bulk | bulk | Australia | 2022-01-29 | Larval | Larval | Liver | Liver and Biliary System |