Samples
Filter metadata by species, assay, tissue and developmental stage. Each record also lists its condition, project and source where available.
Data structure
Downloads
Download catalog metadata, displayed analysis results and reproducible workflow examples.
Sources & references
Trace assemblies to public accessions or see when a dataset remains restricted or metadata-only.
Data scope and count definitions
The genome catalog contains — maple-family nuclear resources (— Acer and — Dipteronia) plus — comparative outgroup resources. Coverage differs by module: orthology covers — genomes, synteny covers —, and PPI covers A. truncatum.
Homepage gene counts refer to primary annotated gene records. Species-card and genome-table counts refer to retained coding models in the integrated annotations. For Ayan, Dipdye, Dipsin and Citsin, these counts exactly match the retained mRNA identifiers, CDS parent identifiers and CDS/protein FASTA identifiers. The available annotations lack a gene hierarchy and filtering history, so these counts do not establish unique biological gene counts or explain every difference from repository annotations. Gene Search uses a broader index that also includes orthology-derived records and transcript models; its records must not be counted as distinct biological genes without resolving those entities.
The sample catalog contains 70 general-expression samples and 134 A. palmatum resequencing records. Its seven tissue categories describe catalog metadata. Seasonal ATAC/WGBS, RNA/Ribo/proteome, leaf-colour and oil datasets are described separately on their module pages. The GWAS panel contains the 70 phenotyped cultivars listed in Table S19 of Ma et al. (2026) and is a subset of the 134-sample VCF. Cohort source records retain the original sample labels.
The general Gene module provides tissue-averaged TPM. Oil and Leaf Color use their own FPKM datasets; their sample sets and units are not interchangeable with the general-expression matrix.
Downloads
Only files with a verified release path are downloadable. Unpublished assemblies are deliberately marked rather than exposed without permission.
Species catalog
Canonical codes, scientific names, assembly statistics, capabilities, accessions, and references.
Synteny index
Validated pair availability and data-file pointers used by the comparative-genomics viewer.
Oil named-sample expression
RNA, Ribo and protein profiles selected by gene ID and sample column name, with source checksums and the exploratory co-expression network. Differential Ribo statistics are excluded pending correction of the imported sample grouping.
Leaf seasonal differential expression
Filtered spring-versus-autumn DEG table used by the Leaf Color page, with gene IDs, seasonal means, log₂ fold changes and FDR values. This file excludes raw reads and genes below the displayed thresholds.
Coverage and source checks
Catalog species and declared capabilities, sample-count definitions, public accession checks and eight recorded differences from current NCBI assembly/annotation metadata. Includes captured metadata, TSVs, checksums and a reproducible build script.
This capture predates the Aneg source-link correction below; its original inputs are retained. Other accession/species matches do not verify the exact assembly version used for local analyses. Unavailable checks and missing reuse terms remain explicitly unknown.
Download catalog snapshot ZIP · Instructions and limits · SHA-256
One gene across modules
Trace Atru.chr5.769_Atru through gene identity, orthogroup membership, tissue TPM, the returned PPI subset and a 1,223 nt genome BLAST match. Includes exact API responses, TSV exports, checksums and a Python script with offline verification.
This is a workflow demonstration, not experimental validation of gene function or a full database release.
Download example ZIP · Instructions and limits · SHA-256 · Open example
Data-processing pipelines
Scripts, tool versions and parameters used to build this release, organized by data type: genomes, orthology and synteny, RNA-seq, ATAC-seq and WGBS, GWAS, multi-omics and database import.
Genome sequence files
Download released FASTA, annotation, CDS, RNA, and protein files from NCBI, Genome Warehouse, or Figshare. Restricted nuclear records remain closed.
Data sources & references
Organellar sequence accessions (16 chloroplast and 5 mitochondrial assemblies)
This table and the Genome page display the same catalog. Public accession identity does not establish that each locally analysed assembly matches the current repository version; see the coverage snapshot for source discrepancies.
| Code / species | Collection | Nuclear accession | Download files | Organelle accessions | Reference | Nuclear release status |
|---|---|---|---|---|---|---|
| Loading references… | ||||||
Correction record — 5 September 2026
Gene identity matching now respects species-qualified IDs. BLAST and primer controls report their actual execution parameters. Oil profiles are rebuilt from named sample columns, with missing values and gene identity preserved across layers.
Seed multi-omics: the six A. truncatum BioSamples comprise three 85-DAF and three 115-DAF seed replicates. Sample source records link RNA-seq and Ribo-seq runs within each BioSample. Per-sample profiles, RNA and protein results are available; gene-level Ribo differential and TE results await validated reanalysis.
Assembly source: the Aneg reference index matches all 108 versioned sequence identifiers and lengths of GCA_025594385.1 (ASM2559438v1). Its catalog accession and download links have been corrected. The initial audit ZIP retains the pre-correction catalog and its eight observed numerical differences. For Ayan, the assembly-size difference is explained by including mitochondrial and chloroplast sequences; several annotation-count and assembly-identity questions remain unresolved. An index match is not a full-file checksum comparison. The retained original delivery MD5 list supplies reference checksums; these have not been verified against every deployed file and do not explain annotation filtering or ID renaming.
Expression sources: A. negundo run SRR17316635 belongs to PRJNA750066. The 16 A. saccharum expression runs remain assigned to PRJNA751902. Their verified project, BioSample and source links are listed in the sample explorer.
Seasonal epigenomics: BioProject PRJNA1163018 contains paired ATAC-seq and WGBS libraries from nine A. palmatum leaf samples (three biological replicates per season). The Epigenome module provides read-weighted CpG methylation summaries and WGBS read-coverage tracks normalized to RPKM in 10-bp bins.
Data-use guidance
For records marked Restricted or Metadata only, request permission and confirm citation or authorship terms before redistribution. Public accessions should be cited together with the original source paper.