The dataset contains the genome and annotation file of Niphotrichum japonicum. The raw data have been deposited in National Genomics Data Center (NGDC; https://ngdc.cncb.ac.cn/bioproject/) under the BioProject accession number PRJCA017860.

Genome assembly and annotation of the allotetraploid wild grass Aegilops ventricosa RM271, which has been published in https://doi.org/10.1016/j.xplc.2024.101131. All the raw sequencing data for Ae. ventricosa RM271 are available in the National Genomics Data Center (https://ngdc.cncb.ac.cn/?lang=en) under BioProject numbers PRJCA018801 (https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA018801).

Northern wild rice (NWR; Zizania palustris L.), an annual aquatic plant in the Poaceae family, has high economic importance due to its nutrient-rich grains. However, the existing NWR genome assembly for this species has severe fragmentation and incomplete gene representation. A near-complete genome was assembled in this study to provide a high-quality genomic reference for NWR-associated research. The assembled genome exhibited a total contig length of 1.41 Gb and a contig N50 of 109.22 Mb. Overall, a 73.60% repetitive sequence content was identified and 47,804 genes predicted. Phylogenetic analysis indicated that Z. palustris was most closely related to Zizania latifolia, with an estimated divergence time of 4.57–8.15 Mya. Meanwhile, Z. palustris underwent a recent, species-specific long terminal repeat (LTR) expansion, associated with its larger genome size. We identified two genomic blocks in the Z. palustris and Z. latifolia genomes that exhibit strong synteny with the rice phytocassane biosynthetic gene cluster. The centromeric satellite repeats in Z. palustris identified in this study primarily comprised a 145 bp repetitive unit. The findings also revealed centromere homogenisation and rearrangement accompanied by LTR invasion in NWR. Among the genes missing in the previous NWR genome, we observed LTR insertion events that resulted in expanded gene lengths in our updated NWR genome. The present updated NWR genome provides a valuable resource for crop genetic improvement, functional gene discovery, and research on critical biological processes.The whole-genome sequence data reported in this paper were also deposited in the Genome Warehouse in National Genomics Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences/China National Center for Bioinformation under accession number GWHFIIQ00000000.1 at https://ngdc.cncb.ac.cn/gwh.

The annotation includes protein-coding genes, ncRNAs, and repeat elements, which are stored in three separate files in gff format. The corresponding genome assembly has been deposited in the GWH database under accession number GWHEUVB00000000.1 and is publicly available at https://ngdc.cncb.ac.cn/gwh.

The tumor ecosystem of papillary thyroid carcinoma (PTC) is poorly characterized. Using single-cell RNA sequencing, we profiled transcriptomes of 158,577 cells from 11 patients’ paratumors, localized/advanced tumors, initially-treated/recurrent lymph nodes and radioactive iodine (RAI)-refractory distant metastases, covering comprehensive clinical courses of PTC.Our study illuminates a comprehensive landscape of PTC ecosystem that suggests potential prognostic and therapeutic implications. Our work not only adds dimensions to the biological underpinnings of PTC heterogeneity, but also provides a benchmark dataset for this malignancy. In total, 23 fresh surgical specimens (7 primary tumors, 6 para-tumors, 8 metastatic LNs and 2 subcutaneous metastatic loci) were collected and subjected to scRNA-seq with 10X Genomics. Submitter declares that the raw data have been deposited in the Genome Sequence Archive (https://ngdc.cncb.ac.cn/gsa/) under submission number HRA001107.

We performed integrative analyses in a Chinese cohort of peri-/post-menopausal women (n = 517) with metagenomics (n = 499), targeted metabolomics (n = 500) and whole-genome sequencing (n = 500) to identify novel microbiome-related biomarkers for bone health. We also performed metagenomics in a US whites cohort for validation (n = 59).The characteristics of the cohorts, genome-wide association study (GWAS) data, concentrations of serum short chain fatty acids (SCFAs), relative abundance of gut microbiota and gut microbiota-associated functional KEGG modules are shown in this dataset.The sequencing data of the Chinese cohort (whole genome sequencing and metagenomics) can be found in “Genome Sequence Archive for Human” (https://ngdc.cncb.ac.cn/gsa-human, accession No. HRA004900). The metagenomic sequencing data can be found in “Sequence Read Archive” (https://www.ncbi.nlm.nih.gov/sra, accession No. PRJNA986283 and PRJNA1011937).

Genome annotation of the assembly for Fulvetta ruficapilla (Fruf_v1).This annotation includes aonnotation for protein-coding genes, ncRNAs, and repetitive elements in three different files in the gff format. The associated genome assembly has been deposited in the GWH database under the accession number GWHETLV00000000.1, publicly available at https://ngdc.cncb.ac.cn/gwh.This version of dataset is provided a natural picture of the species Fulvetta ruficapilla as the cover image, which is taken by authors of the dataset.

Platycodon grandifloras genome annotationpasa2.longest.filter-update-v2.gff3 corresponds to the reference genome publicly available at https://ngdc.cncb.ac.cn/gwh (GWH: GWHARYT00000000.1).

Genomic DNA from G. inflata was extracted by using phenol/ chloroform method, and purified DNA was quantified using a Qubit (Thermo Fisher Scientific). A total of 5 μg genomic DNA was sheared to ~200 bp fragments; the repaired ends were ligated Illumina-based sequencing adaptors to construct an adaptor-ligated DNA library.The ORF sequence of GiMYB76 was fused with the Halo affinity tag and expressed in vitro using TNT® SP6 Coupled Wheat Germ Extract System (Promega, Fitchburg, WI, USA). The fusion protein was bound to magnetic Halo Tag ligand (chloroalkane) beads, isolated from the expression mixture, and verified by Western blotting with anti-Halo Tag antibody (Promega), with nonspecific proteins were washed away. HaloTag-GiMYB76 fusion proteins were incubated with 500 ng of adaptor-ligated genomic DNA library at 30 ℃ for 2 h. Unbound DNA fragments were removed by washing, and samples were heated at 98 ℃ for 10 min to release GiMYB76 bound DNA The recovered DNA was amplified by PCR using indexed TruSeq primers. Indexed DNA samples were subsequently pooled and size-selected to remove residual adaptor dimers. Purified DNA libraries were subjected to next generation sequencing (PE150).The DAP-Seq data used in this study are also available from the National Genomics Data Center (https://ngdc.cncb.ac.cn/; PRJCA039808).

Dataset Description - Version 1

This dataset contains:

Network files:

• mGRN.csv (12.33 MB) - Tissue-specific networks (root, ear, tassel, seed, stem, leaf)

Transcription factor data:

• 405_TFs_motif.rar (163.28 KB) - Transcription factor motif data
• 513_TFs_peak_filter files - Peak files for 513 transcription factors (before and after regulatory region filtering)

Functional analysis:

• GO term enrichment results (17.02 MB)
• Regulatory region analysis (14.24 MB)

Resources:

• Analysis code: https://github.com/Huo-qiang/accuracy-enhanced-maize-gene-regulatory-network-mGRN
• IGV browser: https://dap-seq.maize-endosperm.cn/
• Raw data:
  • https://ngdc.cncb.ac.cn/gsa/browse/CRA022036
  • https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201701

⚠️ Note: An updated version (v2) with additional ChIPSeeker annotation files is available at: https://doi.org/10.5281/zenodo.16029269

Citation:
If you use the data or code, please cite: Huo Q., Zhang Z., Zhang K., Wang Q., Zhang W., Ye X., Lyu Q., Galbraith D.W., Ma Z., and Song R. (2025). Exploring the maize transcriptional regulatory landscape through large-scale profiling of transcription factor binding sites. Mol. Plant. 18, 1777–1798. doi: https://doi.org/10.1016/j.molp.2025.08.009

Raw sequence data of mitochondrial genomes from Pennisetum glaucum ‘23A’ and ‘23B’ based on Illumina NovaSeq 6000 and PacBio Sequel II platforms. The data are also publicly accessible at https://ngdc.cncb.ac.cn/gsa.