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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 19, 2023 |
| Title |
Caffeine, Rep 1 |
| Sample type |
SRA |
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| Source name |
whole larvae (30)
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| Organism |
Danio rerio |
| Characteristics |
tissue: whole larvae (30)
strain: AB strain
treatment: Caffeine (100 mg/l, 0.5 h)
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| Treatment protocol |
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]).
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| Growth protocol |
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.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
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.)
The poly(A)+ RNA libraries were generated using TruSeq RNA Library Prep Kit v2 and sequenced at the Technion Genome Center, Israel.
poly(A)+ RNA-seq. 51 nucleotides single-end runs.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
FastQC, version v0.11.9
BOWTIE2 for read alignment and RSEM software for annotation and expression calculation (https://bioinformaticshome.com/tools/rna-seq/descriptions/RSEM.html).
Assembly: Danio_rerio.GRCz11.dna.primary_assembly.fa.gz
Supplementary files format and content: result files of RSEM software for each sample, one of genes and one of isoforms
Supplementary files format and content: Result files contain gene id, transcript id(s), length, effective length, expected count, TPM and FPKM.
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| Submission date |
Jul 05, 2022 |
| Last update date |
Jul 19, 2023 |
| Contact name |
Ari Meerson |
| E-mail(s) |
arim@migal.org.il
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| Phone |
972-4-6955022
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| Organization name |
MIGALGalilee Research Institute
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| Street address |
2 Tarshish St.
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| City |
Kiryat Shmona |
| ZIP/Postal code |
11016 |
| Country |
Israel |
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| Platform ID |
GPL18413 |
| Series (2) |
| GSE207457 |
Transcriptome profiles of zebrafish larvae from a caffeine-induced anxiety model and a high fat-diet induced obesity model [RNA-Seq] |
| GSE207550 |
Transcriptome profiles of zebrafish larvae from a caffeine-induced anxiety model and a high fat-diet induced obesity model |
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| Relations |
| BioSample |
SAMN29499928 |
| SRA |
SRX16019724 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6287849_results_caf4.genes.results.gz |
708.9 Kb |
(ftp)(http) |
RESULTS |
| GSM6287849_results_caf4.isoforms.results.gz |
1.0 Mb |
(ftp)(http) |
RESULTS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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