The limitations of traditional bulk and single-cell

The gap

Evidence profile

Sourced from the stated research gap and limitations 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 High-Resolution Stereo-Seq Spatial Transcriptomic Resource for Adult Holstein Cattle Liver (2026) · International Journal of Molecular Sciences · doi

  The limitations of traditional bulk and single-cell approaches in characterizing the liver's spatial molecular architecture. The need for a refined reference-guided workflow to overcome standard annotation limitations in livestock. The lack of a high-resolution spatial transcriptomic resource for adult Holstein cattle liver.

  generalstated research gap
  Keywords: limitations traditional bulk single-cell approaches characterizing liver spatial
• 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.

  generallimitationsevidence 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.

  generallimitationsevidence 5/5
  Keywords: cell slan like functional needed role described atlas further myeloid type transcriptional ling single additional

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