run_metadata: 70554
This data as json
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| 70554 | SRR19996289 | SRX16037364 | SRS13717220 | SRP385069 | PRJNA856147 | Transcriptome profiles of zebrafish larvae from a caffeine induced anxiety model and a high fat diet induced obesity model [miRNA Seq] | GSE207549 | Transcriptome Analysis | Obesity associates with anxiety disorders in adult humans rodents and fish although there is also evidence to the contrary. Moreover it is unknown if this association is developmentally regulated and which genes are involved. RNA sequencing differences between caffeine induced anxious zebrafish larvae which exhibited greater thigmotaxis erratic swimming and higher whole body cortisol levels than matched controls and high fat diet fed obese larvae with more numerous and larger peritoneal adipocytes than standard diet controls were revealed. There were 231 polyA+ genes common to both models padj<0.05 and 75% of the transcripts upregulated >1.5 fold in the anxiety model were downregulated <0.67 fold in obese larvae. Immune system pathways were overrepresented among these inversely regulated genes. Overall design: Profile analyses of RNA seq polyA+ and miRNA data were carried out on two zebrafish larval models 15 dpf one of anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and the other of obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. Both models were optimized and validated the anxiety model by behavioral and cortisol level tests and the obesity model by histology based adiposity analysis. RNA was extracted from pools of 30 larvae per replicate 3 replicates per treatment [NO CAF SD HFD] euthanized by ice cold water and snap frozen in liquid nitrogen. | parent bioproject:PRJNA856140 | pubmed:37443828 | Standard diet rep 3 [miRNA Seq] | GSM6294385 | source name:whole larvae 30|tissue:whole larvae 30|strain:AB strain|treatment:Standard diet|geo loc name:missing|collection date:missing | Standard diet rep 3 [miRNA Seq] | Processing was by the Technion Genome Center Israel and the online CLC Genomics Workbench 20.0.3. Library quality control: FASTQC version 0.11.5. Reads were trimmed using the online CLC Genomics Workbench which included removal of the Qiagen three prime adapter on the three prime end. Reads without xxx adapter were discarded and only sequences between 15 and 54 nucleotides were retained. These trimmed files read lengths of 23 bases were joined. miR quantify was run on these files using the reference miRbase v.22.1 and the preference Danio rerio. Normalization was executed using TMM trimmed mean of M values. Annotation was carried out using Go Mapping RNAcentral v10. Supplementary files format and content: excel file with Max Group Mean Log2 Fold change Fold change p Value FDR pvalue Bonferroni for each miR in each model. | whole larvae 30 | anxiety induced by a half hour exposure to 100 mg/liter caffeine [CAF] compared to no treatment [NO] and obesity induced by feeding 6 dpf larvae a high fat diet [HFD egg yolk based] until 15 dpf compared to a standard diet [SD]. | Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs | Kept under 14 h light/10 h dark regimen. Water was pH7 7.7 27.7 28.3 C 490 510 uS/cm. SD was Gemma micro 75 for larvae and 300 for adults. | tissue:whole larvae 30|strain:AB strain|treatment:Standard diet | GSM6294385 | GSM6294385: Standard diet rep 3 [miRNA Seq]; Danio rerio; miRNA Seq | GSM6294385 r1 | GSM6294385 | 1 | Extractions were preceded by homogenization using a motorized pestle and at least 10 subsequent passages through a syringe needle 20 G. Kit used was Nucleospin® miRNA kit Macherey Nagel GmbH & Co. Twelve libraries were generated using QIAseq miRNA Library Kit and sequenced at the Technion Genome Center Israel. miRNA seq including other small RNAs. 75 nucleotide single end runs | miRNA-Seq | TRANSCRIPTOMIC | size fractionation | SINGLE | ILLUMINA | Illumina HiSeq 2500 | SRP385069 | SD3_TTGGACCT_L001_R1_001.fastq.gz | fastq | 1112575856.0 | 14639156.0 | GSM6294385 r1 | 0:76 1:0 | A:332460940;C:266146733;G:266385877;T:247560550;N:21756 | 76 | 0 | 332460940 | 266146733 | 266385877 | 247560550 | 21756 | SRX16037364 | SRS13717220 | SRA1449581 | MIGALGalilee Research Institute | MIGALGalilee Research Institute | 1 | 0.72337 | 0.15566 | 0.8888 | 0.58805 | 76 | B | usable mapping rate | illumina | hiseq_era | 3prime | size_fractionation | unknown | bulk | unknown | unknown | Israel | 2022-07-06 | Multi-stage | Multi-stage | Whole Organism | All anatomical structures |