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| Status |
Public on Mar 06, 2024 |
| Title |
Male, WT, old sample 16 |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Nothobranchius furzeri |
| Characteristics |
tissue: Liver
Sex: Male
age: 25-week old
genotype: WT
batch: 3
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| Growth protocol |
Male or female killifish were fed ad libidum.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fish were euthanized in 500 mg/L of Tricaine (Sigma-Aldrich, A5040) in system water. Dissections were carried out under a stereo binocular (Leica S9D) at room temperature. Livers were collected and flash frozen in liquid nitrogen and kept in -80°C until use. Tissues were homogenized by metal beads in 300 μl of TRI reagent (Sigma-Aldrich, T9424), using a TissueLyzer LT (QIAGEN, #85600) with a dedicated adaptor (QIAGEN, #69980). RNA purification was performed using the Direct-zol RNA Miniprep kit (Zymo, R2052) according to the manufacturer’s instructions. RNA concentration and quality were determined by using an Agilent 2100 bioanalyser (Agilent Technologies).
Library preparation was performed using KAPA Stranded mRNA-Seq Kit (ROCHE-07962193001) according to the recommended protocols. Library quantity and pooling were measured by Qubit (dsDNA HS, Q32854), Size selection at 4% agarose gel. Library quality was measured by Tape Station (HS, 5067-5584). Libraries were sequenced by NextSeq 2000 P3, 50 cycle, 70 bp single-end (Illumina, 20046810) with ~35 million reads per sample.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
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| Description |
Male, WT, old
Male, WT, old
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| Data processing |
Quality control and adapter trimming of the fastq sequence files were performed with FastQC (v0.11.8), multiQC (v1.12), fastx-toolkits (v0.0.13), Trim Galore! (v0.6.4), and Cutadapt (v3.4). 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 using STAR 2.7.6a. Differential gene expression as a function of genotype was performed using the edgeR package (v3.32.1).
Assembly: Nfu_20140520
Supplementary files format and content: CSV file included raw counts for each sample.
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| Submission date |
Nov 27, 2023 |
| Last update date |
Mar 06, 2024 |
| Contact name |
Itamar Harel |
| E-mail(s) |
itamarh@mail.huji.ac.il
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| Organization name |
The Hebrew University of Jerusalem
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| Department |
Genetics
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| Lab |
Harel
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| Street address |
Givat Ram
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| City |
Jerusalem |
| ZIP/Postal code |
9190401 |
| Country |
Israel |
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| Platform ID |
GPL33195 |
| Series (2) |
| GSE248739 |
The germline regulates longevity and somatic repair in a sex-specific manner (RNA-Seq) |
| GSE248741 |
The germline regulates longevity and somatic repair in a sex-specific manner |
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| Relations |
| BioSample |
SAMN38454092 |
| SRA |
SRX22655673 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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