D3G provides a set of genomic data to support development of oligonucleotide therapeutics. It consists of data derived from own experiments as well as publicly available databases, where genome sequences, gene models, and expression data sets are compiled for five species, human, crab-eating macaque, common marmoset, mouse, and rat.
Here we open our original data sets to support development of oligonucleotide therapeutics under CC-BY. We encourage anyone (for example, in academic institute, commercial company, regulatory agency, or others) to use the data sets freely for development or assessment of drugs.
Meanwhile, we request users to respect the embargo on the publication of genome-wide analysis based on this data set, as we are currently preparing manuscripts to provide genome-scale analysis of the non-human primates with complete description of the experimental and computational details with raw data. Exceptions to the policy are for analyses on a couple of locus, gene families, and oligonucleotide sequences, rather than comprehensive large-scale analysis.
The genome assemblies of crab-eating macaque, a polished version of the ones previously described 1, has been registered as GCF_012559485.2 and gene models are constructed by the RefSeq team. The data files, genome assemblies and gene models, are directly downloaded from NCBI and compiled for D3G. Expression data for crab-eating macaque and common marmoset is based on our own CAGE data profiles. The other data sets, reference genome 2 and gene models (RefSeq 3 and Gencode 4) for human, mouse, and rat) were obtained from the UCSC Genome Browser Database on Feb 2022.
|-- calJac4 | |-- expression | | |-- calJac4_ncbiRefseqPromoterExpCounts.txt.gz | | `-- calJac4_ncbiRefseqPromoterExpCpm.txt.gz | |-- gene | | |-- calJac4_Trac2202.bed12.gz | | |-- calJac4_ncbiRefSeq.bed12.gz | | |-- calJac4_ncbiRefSeq_prespliced.fa.gz | | `-- calJac4_ncbiRefSeq_spliced.fa.gz | `-- genome | `-- calJac4.fa.gz |-- hg38 | |-- gene | | |-- hg38_ncbiRefSeqCurated.bed12.gz | | |-- hg38_ncbiRefSeqCuratedProteinCoding.bed12.gz | | |-- hg38_ncbiRefSeqCuratedProteinCoding_prespliced.fa.gz | | |-- hg38_ncbiRefSeqCuratedProteinCoding_spliced.fa.gz | | |-- hg38_ncbiRefSeqCurated_prespliced.fa.gz | | |-- hg38_ncbiRefSeqCurated_spliced.fa.gz | | |-- hg38_ncbiRefSeqPredicted.bed12.gz | | `-- hg38_wgEncodeGencodeCompV39.bed12.gz | `-- genome | `-- hg38.p13.fa.gz |-- macFasRKS1912v2 | |-- expression | | |-- macFasRKS1912v2_ncbiRefseqPromoterExpCounts.txt.gz | | `-- macFasRKS1912v2_ncbiRefseqPromoterExpCpm.txt.gz | |-- gene | | |-- macFasRKS1912v2_Trac2202.bed12.gz | | |-- macFasRKS1912v2_ncbiRefSeq.bed12.gz | | |-- macFasRKS1912v2_ncbiRefSeq_prespliced.fa.gz | | `-- macFasRKS1912v2_ncbiRefSeq_spliced.fa.gz | `-- genome | `-- macFasRKS1912v2.fa.gz |-- md5sum.txt |-- mm39 | |-- gene | | |-- mm39_ncbiRefSeqCurated.bed12.gz | | |-- mm39_ncbiRefSeqCuratedProteinCoding.bed12.gz | | |-- mm39_ncbiRefSeqCuratedProteinCoding_prespliced.fa.gz | | |-- mm39_ncbiRefSeqCuratedProteinCoding_spliced.fa.gz | | |-- mm39_ncbiRefSeqCurated_prespliced.fa.gz | | |-- mm39_ncbiRefSeqCurated_spliced.fa.gz | | |-- mm39_ncbiRefSeqPredicted.bed12.gz | | `-- mm39_wgEncodeGencodeCompVM28.bed12.gz | `-- genome | `-- mm39.fa.gz |-- release_22.02.txt `-- rn7 |-- gene | |-- rn7_ncbiRefSeqCurated.bed12.gz | |-- rn7_ncbiRefSeqCuratedProteinCoding.bed12.gz | |-- rn7_ncbiRefSeqCuratedProteinCoding_prespliced.fa.gz | |-- rn7_ncbiRefSeqCuratedProteinCoding_spliced.fa.gz | |-- rn7_ncbiRefSeqCurated_prespliced.fa.gz | |-- rn7_ncbiRefSeqCurated_spliced.fa.gz | `-- rn7_ncbiRefSeqPredicted.bed12.gz `-- genome `-- rn7.fa.gz
.fa.gz suffix in their names contain nucleotide sequences in FASTA format, ones with
.bed12.gz suffix contain exon-intron structure of gene models in BED12 format (BED format with 12 columns), and ones with
.matrix.txt.gz suffix contain tab-delimited text of expression intensities.
Nucleotide sequences for gene models are compiled by using their genomic coordinates and the genome sequences, only for a selected subset of the gene models. Files containing
prespliced in their names represent immature transcripts before splicing, the same to pre-mRNA for protein coding transcripts (the term “pre-spliced” is used to be compatible with long noncoding RNAs). Note that the protein coding transcripts here include ones on both nuclear and mitochondrial DNAs. It means that protein coding transcripts compiled based on RefSeq [^2] includes
YP_ (for human) or
NP_ (for mouse) entries in addition to
Identifier (ID) for RefSeq gene models consists of
REFSEQ_TRANSCRIPT_ID|GENE_SYMBOL;ENTREZ_GENE_ID, as seen in the example of
NM_000454.4|SOD1;6647 in the
hg38NcbiRefSeqCurated.bed12.gz file. In FASTA files of nucleotide sequences, other information such as genomic coordinates are concatenated after
As for expression data , files containing
ExpCounts in their names represent counts of 5'-ends of CAGE read alignments with the genome sequences, and the ones with
ExpCpm represent expression intensities where the read counts were normalized by CPM, counts per million with RLE (relative log expression) method 5. The files which names include ‘ncbiRefseqPromoter’ indicate promoter level expression data (according to CAGE peaks) of RefSeq gene models (not CAGE peaks).
We generated the following data to construct 5'-end complete gene models by a novel approach (TRaC, Transcript models based on RNA-seq, CAGE, and long read sequencing by Oxford Nanopore sequencing).
The original data is made in a collaboration among RIKEN PMI, RIKEN IMS, Shiga University of Medical Science, CIEA (Central Institute for Experimental Animals), Keio University, RIKEN BDR, DBCLS (Database Center for Life Science), NIBIOHN (National Institutes of Biomedical Innovation, Health and Nutrition), and TMIMS (Tokyo Metropolitan Institute of Medical Science). Please contact us via e-mail below for any questions, comments, suggestions, or collaboration:
Please refer our database like this:
D3G: Database for Drug Development based on Genome and RNA sequences, https://d3g.riken.jp, 2022
We thank to AMED (Japan Agency for Medical Research and Development), NIHS (National Institute of Health Sciences), JPMA (Japan Pharmaceutical Manufacturers Association), and the FANTOM consortium for relevant advices and fruitful discussion. The experiments and the database is financially supported by AMED under Grant Number JP17kk0305008 and JP20kk0305013.
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