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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 28, 2023 |
| Title |
Eggs, fertilized with UV irradiated sperm, rep2 |
| Sample type |
SRA |
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| Source name |
rainbow trout from Rutki strain
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| Organism |
Oncorhynchus mykiss |
| Characteristics |
tissue: oocytes/eggs
cell line: gametes
cell type: eggs
genotype: XX, Doubled Haploids
treatment: fertilzed with UV irradiated sperm (G)
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Eggs preserved in RNA-later solution were incubated overnight in a refrigerator (4 °C) and finally stored at −80 °C until RNA purification. Two to three eggs, depending on their size, were used for RNA isolation for the transcriptomic study. RNA was isolated as previously described (Ocalewicz et al. 2019) using modified TRIzol procedure established at the Igor Babiak laboratory, University of Nordland, Norway. The quality of the obtained RNA was established using TapeStation4150 (Agilent Technologies) and RNA ScreenTape Assay allowing RIN (RNA Integrity Number) evaluation.
Good quality isolates (RIN>8) were quantified using Qubit™ RNA Assay Kits (Thermo Scientific) and 250 ng of a total RNA was used for library preparation with Illumina Stranded mRNA Prep kit (Illumina) and standard protocol. The final libraries were controlled for quality using D1000 Agilent ScreenTapes and TapeStation4150 system, and quantified using Qubit™ dsDNA BR Assay Kit (Thermo Scientyfic). Equimolar pool of libraries was finally commercially sequenced on NovaSeq6000 System (Illumina) in a paired-end read of 2x150 bp to obtain a high sequencing depth (i.e. minimum of 75M PE reads per sample).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: OmykA_1.1
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)
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| Submission date |
Feb 15, 2023 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Artur Gurgul |
| E-mail(s) |
artur.gurgul@urk.edu.pl
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| Organization name |
University of Agriculture in Krakow
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| Department |
Center for Experimental and Innovative Medicine
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| Street address |
Rędzina 1C
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| City |
Kraków |
| ZIP/Postal code |
30-248 |
| Country |
Poland |
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| Platform ID |
GPL29994 |
| Series (1) |
| GSE225353 |
Fishing for genes that affect efficiency of gynogenesis in rainbow trout (Oncorhynchus mykiss) |
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| Relations |
| BioSample |
SAMN33314599 |
| SRA |
SRX19380472 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7047208_G_18.txt.gz |
225.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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