- Whitehead Lab GitHub
- Good Work Habits
- RNA Extraction From Tissue Samples 96-well format
- RNA Extraction From SMALL Tissue Samples 96-well format
- Experimental Design Template
- 2015 Atlantic killifish (Fundulus heteroclitus) reference genome assembly (female fish from Maine) Genome Assembly Fundulus_heteroclitus-3.0.2 at NCBI (BioProject PRJNA177717, BioSample SAMN03277211), as reported in Reid et al 2017.
- 2020 Atlantic killifish (Fundulus heteroclitus) reference genome assembly (male fish from Georgia) Genome Assembly MU-UCD_Fhet_4.0 at NCBI (BioProject PRJNA597160, BioSample SAMN13668183).
- Atlantic killifish (Fundulus heteroclitus) genetic map on EBI BioStudies Accession S-BSST163.
- Atlantic killifish (Fundulus heteroclitus) RAD-seq VCF and phenotype data for Brennan et al 2018 on EBI BioStudies Accession S-BSST168. Raw RAD-seq reads for this study are at NCBI SRA BioProject PRJNA428529.
- Atlantic killifish (Fundulus heteroclitus) Raw RAD-seq reads for Healy et al 2018 are at NCBI SRA BioProject PRJNA477712.
- Atlantic killifish (Fundulus heteroclitus) whole genome resequencing data for Reid et al 2016: NCBI PRJNA323589. SRA RunSelector for data from all 384 samples.
- Atlantic killifish (Fundulus heteroclitus) RNA-seq data for Reid et al 2016: NCBI, GEO GSE156460.
- Whole-genome Nanopore assemblies for additional killifish species (F. catenatus, F. nottii, F. olivaceus, Adinia xenica). Keep up with what we are doing, including data availability, here. Rough assemblies available here, publication here.
- Mangrove killifish (Kryptolebias marmoratus) skin RNA-seq data from emersion challenge experiment, in NCBI SRA BioProject PRJNA448276 (78 samples). A GitHub repo has been created for the timecourse analysis of gene expression.
- Red abalone (Haliotis rufescens) multi-tissue RNA-seq (Illumina). Tissues include 13 tissues from a single female, two tissues from a single male, and from pools of individuals from each of four early-life developmental stages. Data are in NCBI SRA BioProject PRJNA488641. Data were used to annotate reference genome reported in Masonbrink et al 2019.
Notes on the Atlantic killifish Genome Assembly and annotations: We created our own annotation of the F. heteroclitus genome (2015 assembly), and this is reported in the Reid et al 2017 Genome Biology & Evolution (GBE) manuscript. NCBI also did their own annotation for this assembly. So there are a couple of options for matching annotations to the reference genome. Use the NCBI RefSeq annotations if you want. They are available online, or you can download it directly from our Google Drive. Alternatively, if you want to use OUR annotations (reported in GBE, and which we think are better), then: