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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 12, 2023 |
| Title |
paternal backcrosses (backcross F1 hybrid x C. carpio), control group, repl. 2 |
| Sample type |
SRA |
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| Source name |
Head kidney
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| Organism |
Carassius gibelio x Cyprinus carpio 'xingguonensis' |
| Characteristics |
tissue: Head kidney
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| Growth protocol |
Catching and artificial breeding
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| Extracted molecule |
total RNA |
| Extraction protocol |
NEBNext Poly(A) mRNA Magnetic Isolation Module
NEBNext Ultra Directional RNA Library Prep Kit for Illumina
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
gibel.featureCounts.tsv
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| Data processing |
Quality check (FastQC v. 0.11.9)
Quality trimming (Trimmomatic v. 0.36, CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35)
Alignment (STAR v. 2.7.3a; employing default parameters, except for --outFilterMismatchNoverLmax 0.1 and --twopassMode Basic)
Quality control after alignment concerning the number and percentage of uniquely- and multi-mapped reads, rRNA contamination, the mapped regions, the read coverage distribution, strand specificity, gene biotypes, and PCR duplication was performed using several tools (RSeQC v. 2.6.2; Picard toolkit v. 2.18.27; Qualimap v. 2.2.2; BioBloom tools v. 2.3.4)
DGE analysis (featureCounts v. 1.6.3 with settings -s 2 -T 10 -F GTF -Q 0 -d 1 -D 25000; DESeq2 v1.20.0)
Functional annotation (KEGG pathway database; clusterProfiler v 3.12.0)
Assembly: ASM336829v1, GCA_000951615.2
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. carpio reference genome
Supplementary files format and content: tab-delimited text file with featureCounts for samples that originated and mapped significantly better on the C. gibelio reference genome
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| Submission date |
Aug 03, 2023 |
| Last update date |
Sep 12, 2023 |
| Contact name |
Jiri Vorel |
| E-mail(s) |
[email protected]
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| Organization name |
Masaryk University
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| Department |
Department of Botany and Zoology
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| Lab |
Parasitology
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| Street address |
Kotlarska 267/2
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| City |
Brno |
| ZIP/Postal code |
61137 |
| Country |
Czech Republic |
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| Platform ID |
GPL33644 |
| Series (1) |
| GSE240031 |
Heterosis versus breakdown in cyprinid hybrids associated with SVCV infection revealed by transcriptome profile analysis of head kidney |
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| Relations |
| BioSample |
SAMN36829867 |
| SRA |
SRX21241667 |
| 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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