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| Status |
Public on Aug 19, 2021 |
| Title |
PN2_rna_liver |
| Sample type |
SRA |
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| Source name |
homogenised adult liver tissue
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| Organism |
Pundamilia nyererei |
| Characteristics |
tissue: liver
Sex: male
type: tank-reared
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| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA extracted using phenol/chlorophorm approach (see SUPP methods)
ribosomal RNA depletion (RiboZero Illumina) followed by Illumina RNAseq stranded library kit, according to manusfacturer's instructions
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Total RNAseq from adult tissue
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| Data processing |
RNAseq reads were mapped to MZ_UMD2a and gene expression values were calculated using kallisto (see SUPP methods)
WGBS reads were mapped to mapped to SNP-corrected genomes (based on MZ_UMD2a) and methylation levels at CG site were called using Bismark after quality check and adaptor seq removeal using TrimGalore (see SUPP Methods). Methylation at CG sites with ≥5 ≤100 non-clonal seq reads averaged across 50bp-long non-slidding windows per species were performed to produce bw files.
Species-specific high-confidence SNP-corrected genome (fa file) was generated for each of the species studied in this study by using published whole genome sequencing dataset (Malinsky et al 2018); see Methods.
DMRs were called using DSS (see SUPP Methods). P<0.05, minimal overall methylation difference across any DMR between any species was >25% (d25pc), ≥4 CpG, ≥50bp and pvalue<0.05 (p005). For DMR calling, all CG sites were used independent of sequencing coverage following DSS recommandations (improved DMR calling).
Genome_build: Maylandia zebra MZ_UMD2a and SNP-corrected genomes
Supplementary_files_format_and_content: tpm for RNAseq (tsv) generated using kallisto, mCG/CG (bigwig) generated using bismark, SNP-corrected genomes (fa)
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| Submission date |
Sep 24, 2020 |
| Last update date |
Aug 19, 2021 |
| Contact name |
Grégoire M Vernaz |
| Organization name |
University of Basel
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| Street address |
Vesalgasse 1
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| City |
Basel |
| ZIP/Postal code |
4051 |
| Country |
Switzerland |
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| Platform ID |
GPL28548 |
| Series (1) |
| GSE158514 |
Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes |
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| Relations |
| BioSample |
SAMN16255261 |
| SRA |
SRX9184867 |
| 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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