 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 23, 2023 |
| Title |
Nfr Liver Young Het Fasted M smp38 |
| Sample type |
SRA |
| |
|
| Source name |
Nfr Liver
|
| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: Liver
age: 6.5 weeks
genotype: APRT heterozygous
feeding condition: Fasted
Sex: Male
|
| Treatment protocol |
Livers were quickly removed, flash frozen in liquid nitrogen, and then stored in -80 until RNA extraction (up to 3months)
|
| Growth protocol |
Male or female killifish were either fed ad libidum, or fasted for 24h before liver extraction. All extraction were performed between 9am and 12pm.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Samples were disrupted by bead beating in 300μl of TriZol (Sigma) and a single 3mm metal bead (Eldan, BL6693003000) using TissueLyzer LT (QIAGEN, #85600) with a dedicated adaptor (QIAGEN, #69980). Beating was performed twice at 50Hz for 2 minutes. RNA extraction was performed with Direct-zol RNA Purification Kits (Zymo). RNA concentration and quality were determined by using an Agilent 2100 bioanalyser (Agilent Technologies).
Library preparation was performed using KAPA mRNA HyperPrep Kit (ROCHE-08105936001) according to the recommended protocols. Library concentrations were measured by Qubit (dsDNA HS, Q32854), and quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 500 high output kit V2, 75 cycle single-end (Illumina, 20024906) using a NextSeq 500 machine (Illumina) with ~30 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Sample 38
|
| Data processing |
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8) (Andrews, 2017) and the Trim Galore! (v0.6.4) (Krueger, 2015) for Cutadapt (3.4)(Martin, 2011). Options were set to remove Illumina TruSeq adapters and end sequences to retain high-quality bases with phred score >20 and a remaining length >20-bp. Successful processing was verified by re-running FastQC.
Reads was mapped and quantified to the killifish genome Nfu_20140520 (Reichwald et al., 2015; Valenzano et al., 2015) using STAR 2.7.6a (Dobin et al., 2013)
Genome_build: Nfu_20140520
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Dec 13, 2021 |
| Last update date |
May 23, 2023 |
| Contact name |
Itamar Harel |
| E-mail(s) |
itamarh@mail.huji.ac.il
|
| Organization name |
The Hebrew University of Jerusalem
|
| Department |
Genetics
|
| Lab |
Harel
|
| Street address |
Givat Ram
|
| City |
Jerusalem |
| ZIP/Postal code |
9190401 |
| Country |
Israel |
| |
|
| Platform ID |
GPL26990 |
| Series (1) |
| GSE190757 |
Genetic perturbation of AMP biosynthesis extends lifespan and restores metabolic health in a naturally short-lived vertebrate |
|
| Relations |
| BioSample |
SAMN23970515 |
| SRA |
SRX13395476 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
