Downloads
Download the data
Everything produced for the prairie and meadow vole genomes.
Genome assemblies
four haplotypes, two per species, chromosome-scale
mMicOch_UCD_v1_hap1.fasta.gz
Prairie vole (Microtus ochrogaster), 26 autosomes plus X and Y. ERZ29502723
FASTA
mMicOch_UCD_v1_hap2.fasta.gz
Prairie vole, second haplotype. ERZ29502724
FASTA
mMicPen_UCD_v1_hap1.fasta.gz
Meadow vole (Microtus pennsylvanicus), 22 autosomes plus X and Y. ERZ29502725
FASTA
mMicPen_UCD_v1_hap2.fasta.gz
Meadow vole, second haplotype. ERZ29502726
FASTA
Gene annotation
gene models for both species, with and without UTRs
prairie_hap1_egapx.gff.gz
First EGAPx round, short-read RNA-seq evidence only. Superseded by v2; use it only to reproduce earlier results.
GFF
meadow_hap1_egapx.gff.gz
First EGAPx round, short-read RNA-seq evidence only. Superseded by v2.
GFF
prairie/complete.genomic.gff.gz
EGAPx v2 on prairie vole hap1. NCBI convention, with mRNA, exon, and CDS features.
GFF
prairie/complete.genomic.with_utrs.gff.gz
The same models with UTR features added by AGAT, for tools that expect them.
GFF
meadow/complete.genomic.gff.gz
EGAPx v2 on meadow vole hap1. NCBI convention, with mRNA, exon, and CDS features.
GFF
meadow/complete.genomic.with_utrs.gff.gz
The same models with UTR features added by AGAT.
GFF
Chromatin contact maps
CiFi and Hi-C contact matrices
prairie_hap1.hic
CiFi proximity-ligation contacts on prairie hap1.
HIC
prairie_hap1.shortread_hic.hic
Proximo Hi-C contacts on prairie hap1.
HIC
meadow_hap1.shortread_hic.hic
Proximo Hi-C contacts on meadow hap1.
HIC
Browser tracks
repeats, duplications, copy number, methylation, read depth
repeatmasker_detailed.bb
RepeatMasker annotations, colored by repeat class.
BIGBED
sedef_sd_bed.bb
SDs >1 kb at >90% identity, with mate coordinates.
BIGBED
prairie.CN.bw
FastCN copy number across the prairie assembly.
BIGWIG
meadow.CN.bw
Meadow vole read depth mapped onto the prairie assembly.
BIGWIG
prairie_hap1.cpg_methylation.bw
5mC fraction from HiFi reads.
BIGWIG
meadow_hap1.cpg_methylation.bw
5mC fraction from HiFi reads.
BIGWIG
prairie_hap1.hifi_coverage.bw
PacBio HiFi read depth.
BIGWIG
prairie_hap1.hic_coverage.bw
Proximo Hi-C read depth.
BIGWIG
Coordinate conversion
UCSC liftOver chains between builds and species
meadow_UCD_v1_to_VGP.liftover_chains.tar.gz
Convert to the VGP meadow reference GCF_037038515.1.
CHAIN
prairie_vole_mMicOch_UCD_vs_Broad_MicOch1.0.liftover_chains.tar.gz
Convert to the previous prairie reference GCF_000317375.1.
CHAIN
Sequencing reads
HiFi, CiFi, Hi-C, Illumina WGS, and RNA-seq
PRJEB108798
HiFi, CiFi, Hi-C, and Illumina WGS for both species and the woodland vole. PRJEB108798
READS
PRJEB89367
Prairie vole brain, liver, testes, and embryo RNA-seq. PRJEB89367
READS