|
| Status |
Public on Aug 19, 2021 |
| Title |
Mapping epigenetic divergence in the massive radiation of Lake Malawi cichlid fishes |
| Organisms |
Astatotilapia calliptera; Maylandia zebra; Diplotaxodon limnothrissa; Aulonocara stuartgranti; Pundamilia nyererei; Rhamphochromis longiceps; Petrotilapia genalutea |
| Experiment type |
Expression profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
|
| Summary |
Whole-genome methylomes and total transcriptomes for muscle and liver tissues of Lake Malawi cichlid species characterised in the context of phenotypic diversification.
|
| |
|
| Overall design |
Biological replicates (≥2) for all RNAseq and WGBS samples. Male, wild-caught samples for all Lake Malawi cichlid species analysed in this study.
|
| |
|
| Contributor(s) |
Vernaz G, Miska EA |
| Citation(s) |
34620871 |
| |
| Submission date |
Sep 24, 2020 |
| Last update date |
Oct 10, 2021 |
| Contact name |
Grégoire M Vernaz |
| Organization name |
University of Basel
|
| Street address |
Vesalgasse 1
|
| City |
Basel |
| ZIP/Postal code |
4051 |
| Country |
Switzerland |
| |
|
| Platforms (11)
|
| GPL25814 |
Illumina HiSeq 2500 (Maylandia zebra) |
| GPL28548 |
Illumina HiSeq 2500 (Pundamilia nyererei) |
| GPL29182 |
Illumina HiSeq 2500 (Diplotaxodon limnothrissa) |
| GPL29183 |
Illumina HiSeq 2500 (Petrotilapia genalutea) |
| GPL29184 |
Illumina HiSeq 2500 (Rhamphochromis longiceps) |
| GPL29185 |
Illumina HiSeq 4000 (Diplotaxodon limnothrissa) |
| GPL29186 |
Illumina HiSeq 4000 (Maylandia zebra) |
| GPL29187 |
Illumina HiSeq 4000 (Petrotilapia genalutea) |
| GPL29188 |
Illumina HiSeq 4000 (Rhamphochromis longiceps) |
| GPL29189 |
Illumina HiSeq 2500 (Aulonocara stuartgranti) |
| GPL29190 |
Illumina HiSeq 4000 (Astatotilapia calliptera) |
|
| Samples (60)
|
|
| Relations |
| BioProject |
PRJNA665493 |
| SRA |
SRP285275 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE158514_AC_SNPcorrected_MZgenome.fa.gz |
297.7 Mb |
(ftp)(http) |
FA |
| GSE158514_AC_l_n2_50bpmean_SNPcorr.bw |
79.3 Mb |
(ftp)(http) |
BW |
| GSE158514_AS_SNPcorrected_MZgenome.fa.gz |
297.6 Mb |
(ftp)(http) |
FA |
| GSE158514_AS_l_n2_50bpmean_SNPcorr.bw |
86.1 Mb |
(ftp)(http) |
BW |
| GSE158514_DL_SNPcorrected_MZgenome.fa.gz |
297.6 Mb |
(ftp)(http) |
FA |
| GSE158514_DL_l_n3_50bpmean_SNPcorr.bw |
88.0 Mb |
(ftp)(http) |
BW |
| GSE158514_DL_m_n2_50bpmean_SNPcorr.bw |
73.2 Mb |
(ftp)(http) |
BW |
| GSE158514_DMR_allMalawi.SNPcorr.bed.txt.gz |
450.8 Kb |
(ftp)(http) |
TXT |
| GSE158514_Liver_GeneExpression_tpm.txt.gz |
1.4 Mb |
(ftp)(http) |
TXT |
| GSE158514_MZ_SNPcorrected_MZgenome.fa.gz |
297.7 Mb |
(ftp)(http) |
FA |
| GSE158514_MZ_l_n3_50bpmean_SNPcorr.bw |
92.1 Mb |
(ftp)(http) |
BW |
| GSE158514_Muscle_GeneExpression_tpm.txt.gz |
1.6 Mb |
(ftp)(http) |
TXT |
| GSE158514_PG_SNPcorrected_MZgenome.fa.gz |
297.7 Mb |
(ftp)(http) |
FA |
| GSE158514_PG_l_n3_50bpmean_SNPcorr.bw |
90.4 Mb |
(ftp)(http) |
BW |
| GSE158514_PG_m_n2_50bpmean_SNPcorr.bw |
74.1 Mb |
(ftp)(http) |
BW |
| GSE158514_RL_SNPcorrected_MZgenome.fa.gz |
297.6 Mb |
(ftp)(http) |
FA |
| GSE158514_RL_l_n2_50bpmean_SNPcorr.bw |
87.1 Mb |
(ftp)(http) |
BW |
| GSE158514_RL_m_n2_50bpmean_SNPcorr.bw |
81.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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