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| Status |
Public on May 17, 2021 |
| Title |
On-liver-rep2 |
| Sample type |
SRA |
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| Source name |
On-liver
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| Organism |
Oreochromis niloticus |
| Characteristics |
generation: ~93
location: Manzala, Egypt
Sex: male
tissue: liver
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| Treatment protocol |
5-10mg of fresh liver tissue were snap-frozen upon dissection and were homogenized and used for RNA extraction.
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| Growth protocol |
Tank-reared, P. nyererei (generation 1; Lake Victoria) and O. niloticus (generation ~93; Manzala, Egypt)
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol (ThermoFisher) and then treated with DNase (TURBO DNase, ThermoFisher) to remove any DNA contamination.
Quality and quantity of total RNA extracts were determined using NanoDrop spectrophotometer (ThermoFisher), Qubit (ThermoFisher) and BioAnalyser (Agilent). Following ribosomal RNA depletion (RiboZero, Illumina), stranded rRNA-depleted RNA libraries (Illumina) were prepped and sequenced (paired-end 75bp-long reads) on HiSeq2500 V4 (Illumina). On average, 11.82±0.42Mio paired-end reads were generated.
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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 |
HISAT2 2.1.0 for the alignment of reads to their respective genomes.
The aligned reads were assembled using Stringtie and their respective reference genome. The assembled transcriptomes for each biological replicate were merged using Stringtie merge utility to produce one transcriptome per tissue per species.
The assembled transcriptomes were filtered to remove unexpressed and duplicated transcripts. Ballgown's v2.10.0 k-mean clustering was used to reduce the number of highly similar transcripts. The transcripts were clustered within each locus and transcripts within each cluster were merged by taking union of the exon-coordinates of the individual transcripts. The minimum number of clusters was used at each locus such that at least 90% of the within-locus variation was retained.
Genome_build: ASM185804v2, PunNye1.0
Supplementary_files_format_and_content: ctab files generated by Stringtie are tab seprated files that include FPKM estimates
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| Submission date |
May 18, 2020 |
| Last update date |
May 18, 2021 |
| Contact name |
Sudhakaran Prabakaran |
| Organization name |
University of Cambridge
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| Department |
Department of Genetics
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| Street address |
Downing Site, CB2 3EH, UK
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| City |
Cambridge |
| ZIP/Postal code |
CB2 3EH |
| Country |
United Kingdom |
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| Platform ID |
GPL23067 |
| Series (1) |
| GSE150744 |
Total RNA sequencing of the liver tissues of Oreochromis niloticus (Nile Tilapia) and of Pundamilia nyerei |
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| Relations |
| BioSample |
SAMN14944466 |
| SRA |
SRX8357805 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4557993_On_liver_with_ref_2_t_data.ctab.txt.gz |
1.0 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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