Genomics Dataset

Varies of the genomics datasets were either integrated directly or following a re-analyzed procedure.

Datasets List

Category NCBI/NGDC Project number1 Sequencing Data Type Re-analyzed By Ref Genome(s) Fully/Partially Integrated
Chen et al. 2021 (PNAS)2 PRJNA558072 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Partially
Cho et al. 2013 (Plos One)3 PRJNA185754 smRNA-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
Fan et al. 2021 (Plant Genome)4 PRJNA626495 smRNA-seq Zhixia Xiao Gmax_Wm82_a4v1 Fully
HML unpublished data (Huang) PRJNA657378 ATAC-seq, ChIP-seq, DAP-seq, RNA-seq NA Gmax_Wm82_a4v1 Fully
HML unpublished data (Yung) PRJNA753632 ChIP-seq, RNA-seq NA Gmax_Wm82_a4v1 Fully
Hossain et al. 2016 (New Phytologist)5 PRJNA354570 WGBS Qianwen Wang Gmax_Wm82_a4v1 Fully
Huang et al. 2021 (Genomics) 6 PRJNA716521 ChIP-seq, RNA-seq NA Gsoja_W05v1 Fully
Ji et al. 2019 (The Plant Cell)7 PRJNA369414 RNA-seq, smRNA-seq, WGBS Qianwen Wang Gmax_Wm82_a4v1 Fully
Jo et al. 2020 (PNAS)8 PRJNA395064, PRJNA395160, PRJNA590535, PRJNA590536, PRJNA590537 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
Kim et al. 2015 (Plant Physiology)9 PRJNA264602 WGBS Qianwen Wang Gmax_Wm82_a4v1 Fully
Lin et al. 2017 (PNAS)10 PRJNA140453, PRJNA140081, PRJNA165677, PRJNA151265, PRJNA165675, PRJNA165677, PRJNA178372 RNA-seq, smRNA-seq, WGBS Qianwen Wang Gmax_Wm82_a4v1 Partially
Lu et al. 2019 (Nature Plants)11 PRJNA527732 ATAC-seq, ChIP-seq, RNA-seq Qianwen Wang Gmax_Wm82_a4v1 Partially
Niyikiza et al. 2020 (The Plant Journal)12 PRJNA560858 RNA-seq, WGBS Qianwen Wang Gmax_Wm82_a4v1 Fully
Pelletier et al. 2017 (PNAS)13 PRJNA389820 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Partially
PRJNA248218 (smRNA) PRJNA248218 smRNA-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA248303 (smRNA) PRJNA248303 smRNA-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA248316 (smRNA) PRJNA248316 smRNA-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA248403 (smRNA) PRJNA248403 smRNA-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA395060 (ABI3) PRJNA395060 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA395102 (bZIP67) PRJNA395102 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA472968 (Histone modification) PRJNA472968 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA558071 (AGL62) PRJNA558071 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA638945 (WRI1) PRJNA638945 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA637947 (GRF5) PRJNA639847 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
PRJNA638949 (HB22) PRJNA638949 ChIP-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
Rambani et al. 2020 (New Phytologist)14 PRJNA534066 RNA-seq, WGBS Qianwen Wang Gmax_Wm82_a4v1 Fully
Song et al. 2013 (Molecular Plant)15 PRJNA156279, PRJNA156281, PRJNA156283 WGBS, smRNA-seq, RNA-seq Qianwen Wang Gmax_Wm82_a4v1 Partially
Wang et al. 2020 (Genomics)16 PRJAN629642, PRJAN629646, PRJAN626514 ChIP-seq, RNA-seq NA Gmax_Wm82_a4v1 Fully
Wang et al. 2021 (The Plant Cell)17 PRJNA657728 ATAC-seq, ChIP-seq, RNA-seq, WGBS Qianwen Wang Gmax_Wm82_a4v1, Gsoja_W05v1 Partially
Lin et al. (Plant Physiology)18 Public Dataset RNA-seq NA Gmax_Wm82_a2v1, Gsoja_W05v1 Partially
Xie et al. 2019 (NC)19 PRJNA48670 RNA-seq NA Gsoja_W05v1 Fully
Huang et al. 2021 (Genes)20 PRJNA7165217 ATAC-seq, ChIP-seq, RNA-seq NA Gsoja_W05v1 Fully
Liu et al. 2018 (PCE)21 PRJNA432861 RNA-seq Qianwen Wang Gmax_Wm82_a4v1 Fully
Shen et al. 2019 (SCI CHINA LIFE SCI)22 PRJCA000902 smRNA-seq, RNA-seq Qianwen Wang Gmax_ZH13_v2 Fully

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  2. Chen M, Lin JY, Wu X, et al. Comparative analysis of embryo proper and suspensor transcriptomes in plant embryos with different morphologies. Proc Natl Acad Sci U S A. 2021;118(6). doi:10.1073/pnas.2024704118 ↩︎

  3. Cho YB, Jones SI, Vodkin L. The Transition from Primary siRNAs to Amplified Secondary siRNAs That Regulate Chalcone Synthase During Development of Glycine max Seed Coats. Freitag M, ed. PLoS One. 2013;8(10):e76954. doi:10.1371/journal.pone.0076954 ↩︎

  4. Fan K, Wong‐Bajracharya J, Lin X, et al. Differentially expressed microRNAs that target functional genes in mature soybean nodules. Plant Genome. 2021;14(2):1-14. doi:10.1002/tpg2.20103 ↩︎

  5. Hossain MS, Kawakatsu T, Kim K Do, et al. Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs. New Phytol. 2017;214(2):808-819. doi:10.1111/nph.14421 ↩︎

  6. Huang M, Zhang L, Zhou L, et al. An expedient survey and characterization of the soybean JAGGED 1 (GmJAG1) transcription factor binding preference in the soybean genome by modified ChIPmentation on soybean protoplasts. Genomics. 2021;113(1):344-355. doi:10.1016/j.ygeno.2020.12.026 ↩︎

  7. Ji L, Mathioni SM, Johnson S, et al. Genome-Wide Reinforcement of DNA Methylation Occurs during Somatic Embryogenesis in Soybean. Plant Cell. 2019;31(10):2315-2331. doi:10.1105/tpc.19.00255 ↩︎

  8. Jo L, Pelletier JM, Hsu SW, Baden R, Goldberg RB, Harada JJ. Combinatorial interactions of the LEC1 transcription factor specify diverse developmental programs during soybean seed development. Proc Natl Acad Sci U S A. 2020;117(2):1223-1232. doi:10.1073/pnas.1918441117 ↩︎

  9. Kim K Do, El Baidouri M, Abernathy B, et al. A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean. Plant Physiol. 2015;168(4):1433-1447. doi:10.1104/pp.15.00408 ↩︎

  10. Lin J-Y, Le BH, Chen M, et al. Similarity between soybean and Arabidopsis seed methylomes and loss of non-CG methylation does not affect seed development. Proc Natl Acad Sci. 2017;114(45):E9730-E9739. doi:10.1073/pnas.1716758114 ↩︎

  11. Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. The prevalence, evolution and chromatin signatures of plant regulatory elements. Nat Plants. 2019;5(12):1250-1259. doi:10.1038/s41477-019-0548-z ↩︎

  12. Niyikiza D, Piya S, Routray P, et al. Interactions of gene expression, alternative splicing, and DNA methylation in determining nodule identity. Plant J. 2020;103(5):1744-1766. doi:10.1111/tpj.14861 ↩︎

  13. Pelletier JM, Kwong RW, Park S, et al. LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development. Proc Natl Acad Sci U S A. 2017;114(32):E6710-E6719. doi:10.1073/pnas.1707957114 ↩︎

  14. Rambani A, Pantalone V, Yang S, et al. Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism. New Phytol. 2020;227(1):168-184. doi:10.1111/nph.16511 ↩︎

  15. Song Q-X, Lu X, Li Q-T, et al. Genome-Wide Analysis of DNA Methylation in Soybean. Mol Plant. 2013;6(6):1961-1974. doi:10.1093/mp/sst123 ↩︎

  16. Wang Q, Yung W, Wang Z, Lam H. The histone modification H3K4me3 marks functional genes in soybean nodules. Genomics. 2020;112(6):5282-5294. doi:10.1016/j.ygeno.2020.09.052 ↩︎

  17. Wang L, Jia G, Jiang X, Cao S, Chen ZJ, Song Q. Altered chromatin architecture and gene expression during polyploidization and domestication of soybean. Plant Cell. Published online March 17, 2021:1-17. doi:10.1093/plcell/koab081 ↩︎

  18. Lin X, Lin W, Ku Y-S, et al. Analysis of Soybean Long Non-Coding RNAs Reveals a Subset of Small Peptide-Coding Transcripts. Plant Physiol. 2020;182(3):1359-1374. doi:10.1104/pp.19.01324 ↩︎

  19. Xie M, Chung CYL, Li MW, et al. A reference-grade wild soybean genome. Nat Commun. 2019;10(1):1-12. doi:10.1038/s41467-019-09142-9 ↩︎

  20. Huang MK, Zhang L, Zhou LM, Yung WS, Li MW, Lam HM. Genomic features of open chromatin regions (Ocrs) in wild soybean and their effects on gene expressions. Genes. 2021;12(5). doi:10.3390/genes12050640 ↩︎

  21. Liu A, Xiao Z, Li MW, et al. Transcriptomic reprogramming in soybean seedlings under salt stress. Plant Cell Environ. 2019;42(1):98-114. doi:10.1111/pce.13186 ↩︎

  22. Shen Y, Du H, Liu Y, et al. Update soybean Zhonghuang 13 genome to a golden reference. Sci China Life Sci. 2019;62(9):1257-1260. doi:10.1007/s11427-019-9822-2 ↩︎