|
| Status |
Public on Jun 09, 2022 |
| Title |
G09E01_wild_Riverine_1_run2_WGBS |
| Sample type |
SRA |
| |
|
| Source name |
homogenized adult liver
|
| Organism |
Astatotilapia calliptera |
| Characteristics |
ecomoprh: Riverine
Sex: male
type: wild caught
tissue: liver
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA extracted using silica column based approach (see methods)
DNA strand-specific library using methylated adaptor (NEB) followed by bisulfite conversion (Imprint, Sigma), according to manusfacturer's instructions. WGBS libraries contain lambda genome spike-in control (0.2% w/w).
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Total DNA from homogenized tissue
Riverine_wild_n2_mCG_50bpBIN_4x.bw
Bisulfite-Seq (whole genome)
|
| Data processing |
RNAseq reads were mapped to MZ_UMD2a and transcript expression values (tpm) were calculated using kallisto (see methods)
WGBS and RRBS reads were mapped to MZ_UMD2a and methylation levels at CG site were called using Bismark after quality check and adaptor seq removeal using TrimGalore (see Methods).
Genome_build: GCF_000238955.4_M_zebra_UMD2a_genomic.fa
Supplementary_files_format_and_content: bw files containing mean mCG/CG levels averaged over 50bp non-overlapping bins and across samples for each group. Only CG with ≥4x coverage were used.
Supplementary_files_format_and_content: GeneQuant_tpm_Masoko_wild_liver.txt contains gene expression values (tpm) for all RNAseq samples.
Supplementary_files_format_and_content: Common_mCG_RRBS.txt file contains methylation values at common CG sites across all RRBS samples (min. 4x coverage in all CGs of all samples)
|
| |
|
| Submission date |
May 09, 2021 |
| Last update date |
Jun 09, 2022 |
| Contact name |
Grégoire M Vernaz |
| Organization name |
University of Basel
|
| Street address |
Vesalgasse 1
|
| City |
Basel |
| ZIP/Postal code |
4051 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL29190 |
| Series (1) |
| GSE174120 |
Epigenetic Divergence during Early Stages of Speciation in an African Crater Lake Cichlid Fish |
|
| Relations |
| BioSample |
SAMN19081021 |
| SRA |
SRX10823664 |
