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. 2024 Mar 26;4(4):100527. doi: 10.1016/j.xgen.2024.100527
REAGENT or RESOURCE SOURCE IDENTIFIER
Deposited data
Structural variants in HXB RI panel (VCF) This paper https://doi.org/10.5281/zenodo.10398554
Join calling of 163 WGS rat samples (VCF) This paper https://doi.org/10.5281/zenodo.10398344
Transcription start site for 2 brain regions This paper https://doi.org/10.5281/zenodo.10398387
Alternative polyadenylation sites This paper https://doi.org/10.5281/zenodo.10398476
Potential misassembled regions This paper https://doi.org/10.5281/zenodo.10428255
Chromosomal dot plots between Rnor_6.0 and mRatBN7.2 This paper https://doi.org/10.5281/zenodo.10515796
The order of genetic markers and the distances from a rat genetic map compared to their locations in Rnor_6.0 This paper https://doi.org/10.5281/zenodo.10552387
The order of genetic markers and the distances from a rat genetic map compared to their locations in mRatBN7.2 This paper https://doi.org/10.5281/zenodo.10552453
Code and data for phylogenetic analysis This paper https://doi.org/10.5281/zenodo.10520242
nucleus accumbens core eQTL dataset Munro et al.30 NAcc, 75 samples
csRNA-seq data Duttke et al.75 N/A
Annotation of the mRatBN7.2 assembly O’Leary et al.76 Release 108
Code and computational notebook This paper https://doi.org/10.5281/zenodo.10552887
Experimental models: Organisms/strains
Sample metadata for RatCollection This paper https://doi.org/10.5281/zenodo.10552790
Software and algorithms
QUAST Mikheenko et al.25 N/A
paftools Kalikar et al.77 N/A
BWA mem Li and Durbin78 N/A
GATK Poplin et al.79 N/A
LongRanger N/A
Minimap2 Li80 N/A
Deepvariant Poplin et al.26 N/A
GLNexus Yun et al.27 N/A
SURVIVOR Jeffares et al.81 N/A
SnpEff Cingolani et al.82 N/A
RepeatMasker Tarailo-Graovac and Chen83 N/A
GeneCup Gunturkun et al.84 N/A
UCSC Liftover tool Hinrichs et al.85 N/A
PLINK Purcell et al.86 N/A
Lep-MAP3 Rastas87 N/A
bcftools Danecek et al.88 N/A
MEGA Tamura et al.89 N/A
ggtree Yu et al.90 N/A
STAR aligner Dobin et al.91 N/A
HOMER’s findPeaks tool Duttke et al.92 N/A
QTLtools Delaneau et al.93 N/A
UniProt UniProt Consortium94 N/A