run_metadata: 66049
This data as json
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| 66049 | SRR15831107 | SRX12122760 | SRS10102619 | SRP336372 | PRJNA762031 | Genetic roles of Hnf4 family transcription factors in zebrafish development and microbial response | GSE183799 | Transcriptome Analysis | The goal of this study was to better understand the roles of Hnf4 fmaily transcription factors in zebrafish development and intestinal function. We used RNA sequencing to compare gene expression changes in digestive tracts dissected from 6dpf larval zebrafish. Our first experiment compared samples from wild type and hnf4g / zebrafish which were either raised germ free or with a conventional microbiota starting at 3dpf. The second experiment compared samples from wild type hnf4g / and hnf4a / ;hnf4g / zebrafish conventionally raised from 0dpf with a microbiota. Each sample consists of RNA extracted from 10 15 pooled gastrointestinal tracts and 4 biological replicates per treatment group were sequenced. Overall design: mRNA profiles of gastrointestinal tracts dissected from 6dpf larval zebrafish from two experiments were analyzed and compared: 1 WTCV WTGF hnf4g / CV hnf4g / GF 2 WTCR hnf4g / CR hnf4a / ;hnf4g / CR | pubmed:36218393 | WTCV 4 | GSM5571373 | source name:dissected GI tract|tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf | WTCV 4 | Paired read files were concatenated in Galazy and trimmed using Trim Galore Reads were mapped to the Danio rerio DanRer11 genome using RNAstar Features counts was used to quanity the number of reads mapped per gene DESeq was used to determine differential gene expression and statisical significance Genome build: DanRer11 Supplementary files format and content: bigwig files were generated in Galaxy based on the BAM file output from RNAstar | dissected GI tract | larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols | tissue:dissected GI tract|genotype:wild type|microbial status:Conventionalized with microbes at 3dpf|age:6 dpf | GSM5571373 | GSM5571373: WTCV 4; Danio rerio; RNA Seq | GSM5571373 | 1 | larval gastrointestinal tracts were dissected and placed directly into TRIZOL reagent; sames were homogenized using a 27Ga needle; and then the PureLink RNA Mini Kit Invitrogen was used to extract total RNA RNA libraries were prepared using standard Illumina protocols | GEO Accession:GSM5571373 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP336372 | loader:fastq load.py | 5872-S15_S15_L002_R1_001.fastq.gz 5872-S15_S15_L002_R2_001.fastq.gz | fastq fastq | 2469415002.0 | 24209951.0 | GSM5571373 r2 | 0:51 1:51 | A:624230763;C:606027471;G:594177750;T:642584632;N:2394386 | 51 | 51 | 624230763 | 606027471 | 594177750 | 642584632 | 2394386 | SRX12122760 | SRS10102619 | SRA1290854 | GEO | Duke University School of Medicine | 2 | 0.96997 | 0.95895 | 0.07801 | 0.0741 | 0.72312 | 0.7234 | 0.55892 | 0.55418 | 51 | 51 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | bulk | bulk | United States | 2021-09-09 | Larval | Larval | Gut | Digestive System |