Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
2016 · paper · Biomedicine
Introduces spatial transcriptomics, which places tissue sections on arrays of barcoded primers so RNA-sequencing data keep their two-dimensional position. The authors demonstrate it on mouse brain and human breast cancer sections.
0 findings
None that passed a second check.
3 minor (typos and the like; most checked by the judge only)
Wording The text describes Doc2g as having "previously known restricted expression ... in the glomerular layer (GL)", yet Fig. 2E lists Doc2g first among the "10 different genes with highly enriched expression in the mitral cell layer (MCL)".
- p. 4 Main text, paragraph on homologous/different domains
Doc2g in the glomerular layer (GL) and Penk in
- p. 3 Fig. 2E heat map gene list (first row) and legend
Lateral diffusion of transcripts from genes enriched in MCL
- p. 2 Main text, last paragraph
10 different genes with highly
Only the authors can say what is right here.
Judge's note: Page 4 text: "previously known restricted expression, such as Doc2g in the glomerular layer (GL) and Penk in the GCL (13)". Page 2 text, last paragraph: "10 different genes with highly enriched expression in the mitral cell layer (MCL)". Page 3, Fig. 2E heat map: Doc2g is the first row, with high log2 counts in the MCL columns, and the legend reads "Lateral diffusion of transcripts from genes enriched in MCL". The paper does not say how one gene is both GL-restricted and highly MCL-enriched, so the layer assignment is unclear. Only the authors can say which layer is meant (or whether both are), so this is a query.
Second check: another model agreed
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Typo Supplementary figure citation "(Fig. 4, C to E, and fig S11)" lacks the period after "fig" (elsewhere "fig. S11C").
- p. 5 Main text, first column, paragraph on ductal cancer in situ areas
(Fig. 4, C to E, and fig S11)
- p. 5 Results/discussion text, left column, breast cancer paragraph
Fig. 4, C to E, and fig S11
Judge's note: The page 5 crop shows "and fig" at the end of one line and "S11)." on the next, with no period. Two lines earlier the same paragraph prints "fig. S11C". This is a cosmetic punctuation error.
Second check: none (judge only)
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Typo Supplementary Materials box reads "Figs. S1 to 11" instead of "Figs. S1 to S11".
- p. 5 Supplementary Materials box, right column
Figs. S1 to 11
Judge's note: The page 5 crop of this paper's Supplementary Materials box (suppl/DC1 for 353/6294/78) shows "Figs. S1 to 11". The text cites fig. S11, and the preceding article's box uses the form "Figs. S1 to S10". This is a cosmetic omission of the S prefix.
Second check: none (judge only)