One limitation of our study is that while the 10X Visium

The gap

Evidence profile

Stated in the limitations and inline gaps sections of the source papers, classified as general, drawn from work published between 2024 and 2026, spanning 3 journals. Those papers have been cited 248 times in total.

Supporting evidence — 3 representative gaps

• A spatially resolved multi-omic single-cell atlas of soybean development (2024) · Cell · cited 97× · doi

  Although we profiled single-cell transcriptome and chromatin accessibility from tissues at the same developmental stage, these two modalities were assessed separately, meaning they were not derived from the same individual cells. Instead, we relied on computational Cell. Author manuscript; available in PMC 2026 January 23. A u t h o r M a n u s c r i p t A u t h o r M a n u s c r i p t A u t h o r M a n u s c r i p t A u t h o r M a n u s c r i p t Zhang (张旋) et al. Page 15 methods to integrate the datasets, which introduces potential limitations due to the inherent complexity and variability of these techniques. Additionally, we used spatial transcriptomics to validate cell type identities in the single-cell datasets. However, the spatial transcriptomics data has a resolution of approximately 50 μm, which is generally larger than single-cell resolution. As a result, the validation is not at the level of individual cells, necessitating the use of prior marker information from other species to aid in the annotation. Although we assume that marker genes are expressed similarly across species, there is a risk of inaccuracies due to functional diversification over evolutionary time. These limitations, particularly the reliance on cross-species markers and the integration of separate modalities, could impact the precision of our findings. Additionally, inaccuracies in gene and transposable element annotations may have impacted our study by misidentifying or omitting key sequence elements, leading to potential misinterpretations of the data. However, we anticipate that future advancements in technology will help overcome these challenges, improving the accuracy and resolution of such studies.

  generalstated in limitationsevidence 5/5
  Keywords: cell single resolution species modalities individual cells datasets potential limitations additionally spatial transcriptomics marker inaccuracies
• An atlas of cells in the human tonsil (2024) · Immunity · cited 151× · doi

  Additional functional studies are needed to decipher the role of multiple cell types described in this atlas. For instance, we foresee that further functional characterization of the slan-like compartment will unravel the specialized functions of the four myeloid subsets we described here. Because the markers of our slan-like clusters partially overlap with macrophage states reported in other efforts, future studies will unequivocally clarify whether slan-like represents a distinct myeloid cell type. Also, further experimental evidence is needed to disentangle the role of the SIX5 TF in PC lineage commitment. While current atlases of healthy human organs and tissues focus on the analysis of mostly transcriptional data, the presented atlas integrated five modalities, including spatially resolved transcriptional profiling. However, currently available ST technologies for transcriptome-wide profiling do not provide bona fide single-cell resolution and require capture site deconvolution to predict cell-type location by integrating single-cell and ST datasets, or analysis must be limited to signature and marker gene visualization.

  generalstated in limitationsevidence 5/5
  Keywords: cell slan like functional needed role described atlas further myeloid type transcriptional ling single additional
• Identification of a long-term surviving human mesenchymal stromal cell subpopulation and implications for recessive dystrophic epidermolysis bullosa treatment (2026) · Stem Cell Research & Therapy · doi

  One limitation of our study is that while the 10X Visium spatial transcriptomics analysis provided a valuable overview of gene expression in the surviving BM-MSC population, it lacks the resolution needed to detect transcriptomic differences at the single-cell level.

  generalstated in inline gapsevidence 5/5
  Keywords: limitation visium spatial transcriptomics provided valuable overview gene expression surviving population lacks resolution needed detect

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