Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
Cell, 2015 · paper · Biomedicine
Describes Drop-Seq, which profiles thousands of individual cells by sorting them into nanoliter droplets and barcoding each cell's RNA. Applied to 44,808 mouse retinal cells, it identified 39 transcriptionally distinct cell populations.
7 findings
Substance The text says Opn4+ RGCs "expressed nine genes at levels two-fold higher than Opn4- RGCs", but the Figure 6H legend says "Seven genes were identified as enriched in Opn4-positive cells (red dots, >2-fold, p<10−9)."
- p. 8 Results, Supervised analysis
(26/432) expressed nine genes at levels two-fold higher than Opn4- RGCs
- p. 25 Figure 6H legend
Seven genes were identified as enriched in Opn4-positive cells (red dots, >2-fold, p<10−9).
- p. 25 Figure 6H legend
Seven genes were identified as enriched in Opn4-positive cells (red dots, >2-fold, p<10−9)
- p. 8 Supervised analysis section
expressed nine genes at levels two-fold higher than Opn4- RGCs
Only the authors can say what is right here.
Judge's note: Text (page 8) and the Figure 6H legend (page 25) describe the same comparison (Opn4+ vs Opn4- RGCs, two-fold) but give 9 and 7 genes. The gene labels in panel H on page 24 are too small to count reliably (roughly 7-8 labels). Only the authors can say which count is right.
Second check: another model agreed
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Reference or label Figure 3C,D legend gives the colours as "54 HEK (human) STAMPs (blue) and 28 3T3 (mouse) STAMPs (green)", but in the published panels the human violins are light grey and the mouse violins dark grey.
- p. 19 Figure 3C,D legend
54 HEK (human) STAMPs (blue) and 28 3T3 (mouse) STAMPs (green)
- p. 18 Figure 3C,D panels
Human / Mouse
- p. 5 Figure 3C,D panels
Human Mouse
Judge's note: On the p18 image, panels C and D show light-grey (Human) and dark-grey (Mouse) violins, while panels A and B on the same page are in colour. The legend on p19 still says blue and green, so the colour key does not match the figure.
Second check: another model agreed
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Reference or label Table S3 is cited for the cell-cycle genes ("(Figure 4C and Table S3)") and also for the retina PCA ("(Figure S5, Table S3)"), while the Figure 4C legend says "A complete list of cell cycle regulated genes can be found in Table S2."
- p. 6 Results, Cell states
(Figure 4C and Table S3)
- p. 6 Results, Cell types
the 13,155 largest libraries (Figure S5, Table S3)
- p. 6 Retina clustering paragraph
(Figure S5, Table S3)
Only the authors can say what is right here.
Judge's note: On page 6, Table S3 is cited both for the novel cell-cycle genes (Fig 4C) and for the PCA of the 13,155 retinal libraries. The Figure 4C legend on page 21 sends the reader to Table S2 for the full list of cell-cycle-regulated genes. Table S2 is also cited for the Whitfield gene sets (page 6 and Methods page 10). So the cell-cycle gene list is pointed to two different tables, and Table S3 is pointed to for two unrelated contents. The supplement is not among the files, so only the authors can say which pointer is right.
Second check: another model agreed
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Reference or label The Figure 4C legend says "A complete list of cell cycle regulated genes can be found in Table S2", but the Results cite "(Figure 4C and Table S3)" for these genes, and Table S2 is elsewhere the phase gene sets.
- p. 21 Figure 4C legend
A complete list of cell cycle regulated genes can be found in Table S2.
- p. 6 Results, Cell states
not previously connected to the cell cycle (Figure 4C and Table S3)
- p. 10 Methods, Cell cycle analysis
with some modification (Extended Experimental Procedures and Table S2)
- p. 6 Results, cell cycle
(Figure 4C and Table S3)
Only the authors can say what is right here.
Judge's note: On p6 the Results cite Table S2 for the Whitfield phase gene sets '(Figure 4A, Table S2)' and Table S3 for the regulated genes. The p10 Methods also tie Table S2 to the phase gene sets. Table S3 is cited again on p6 for the retina PCA '(Figure S5, Table S3)'. The pointers are inconsistent. The supplement is not among the files, so which table is meant cannot be settled here.
Second check: another model agreed
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Reference or label "(Jeon et al., 1998) (Table 1)" and "population (1%, Table 1)" cite a Table 1 that does not appear anywhere in the 25-page manuscript.
- p. 7 Results
with earlier estimates from microscopy (Jeon et al., 1998) (Table 1).
- p. 8 Results, Supervised analysis
population (1%, Table 1)
- p. 7 Results, retina
agreed with earlier estimates from microscopy (Jeon et al., 1998) (Table 1)
- p. 8 Results, supervised analysis
(1%, Table 1)
Only the authors can say what is right here.
Judge's note: Table 1 is cited on pages 7 and 8. Pages 14-25 contain the end of the reference list, then Figures 1-6 and their legends only; the text layer has no table caption at all. The cited table cannot be checked. The 1% RGC figure is consistent with the 432 RGCs out of 44,808 cells.
Second check: another model agreed
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Reference or label The Figure 3F y-axis is labelled "mRNA-seq [log(1 + RPKM)]", but the legend says "All expression counts were converted to average transcripts per million (ATPM) and plotted as log (1+ATPM)."
- p. 18 Figure 3F y-axis
mRNA-seq [log(1 + RPKM)]
- p. 19 Figure 3E,F legend
All expression counts were converted to average transcripts per million (ATPM) and plotted as log (1+ATPM).
Only the authors can say what is right here.
Judge's note: The page 18 image shows the RPKM y-axis in panel F; panel E and both x-axes use ATPM. The legend on page 19 says all counts are in ATPM. Either the axis label or the legend is wrong.
Second check: another model agreed
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Reference or label Figure 5E legend reads "tSNE plot from Figure 2B, with each cell now colored by experimental replicate"; the retina tSNE plot is Figure 5B, while Figure 2B is the microfluidic device photo.
- p. 23 Figure 5E legend
tSNE plot from Figure 2B, with each cell now colored by experimental replicate
- p. 23 Figure 5E legend
tSNE plot from Figure 2B
Judge's note: On p16, Figure 2B is a photograph of the microfluidic device, and Figure 2 contains no tSNE. On p22, Figure 5B is the tSNE of the 44,808 cells, and panel E reproduces that layout. The pointer should read Figure 5B.
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12 minor (typos and the like; most checked by the judge only)
Wording The text says MitoP "has been shown to express cyan fluorescent protein (CFP) specifically in nGnG amacrines", but the Figure 6F legend says the mice "express CFP in both nGnG amacrines and type 1 bipolars".
- p. 8 Results, amacrines
has been shown to express cyan fluorescent protein (CFP) specifically in nGnG amacrines
- p. 25 Figure 6F legend
which express CFP in both nGnG amacrines and type 1 bipolars
Judge's note: Both statements were checked on pages 8 and 25. The text probably means specific among amacrines, since it goes on to say "CFP-positive amacrines". As worded, though, it conflicts with the legend.
Second check: another model agreed
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Wording Figure 6 title "Finer-scale expression distinctions among amacrine cells, cones and retinal ganglion cells" names cones, but no panel or legend item covers cones.
- p. 24 Figure 6 title
Finer-scale expression distinctions among amacrine cells, cones and retinal ganglion cells
Only the authors can say what is right here.
Judge's note: On the p24 image, panels A–G deal with amacrine cells and panel H with Opn4+ vs Opn4− RGCs. The legend for panels A–H (pp24–25) never mentions cones. The title therefore describes content the figure does not have, and the authors should say whether a panel was dropped.
Second check: another model agreed
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Typo The reference reads "Umbanhowar PBPV, Weitz DA." and is cited in the text as "(Umbanhowar, 2000)".
- p. 13 Reference list
Umbanhowar PBPV, Weitz DA.
- p. 2 Introduction
(Thorsen et al., 2001; Umbanhowar, 2000)
- p. 13 Reference list
Umbanhowar PBPV, Weitz DA. Monodisperse Emulsion Generation
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that the co-author 'Prasad V' has been merged into Umbanhowar's initials. From the files alone, the entry lists at least two authors, yet the citation on page 2 is single-author. Elsewhere the paper writes 'X and Y, year' for two authors (e.g. 'Vogelstein and Kinzler, 1999'). Checked on pages 2 and 13.
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Typo "(p < 10^9, Figure 6H)" is missing the minus sign in the exponent; the Figure 6H legend gives p<10−9.
- p. 8 Results, Supervised analysis
(p < 10<sup>9</sup>, Figure 6H)
Judge's note: The page 8 image and its zoomed crop show a superscript 9 with no minus sign. Other exponents on the same page (p<10−9) do show the minus, and so does the Figure 6H legend on page 25. This is a typesetting slip with an evident fix.
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Typo The transgenic line is spelled "MitoP" in the text (page 8) and "Mito-P" in the Figure 6F legend (page 25).
- p. 8 Results
We used a transgenic strain (MitoP)
- p. 25 Figure 6F legend
fixed adult retina from Mito-P mice
- p. 8 Amacrine text
transgenic strain (MitoP)
- p. 25 Figure 6F legend
Mito-P mice
Judge's note: Both spellings were checked on the page images. This is a cosmetic inconsistency.
Second check: none (judge only)
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Typo "Klein et al. (Klein, 2015)" uses a single-author parenthetical for a nine-author reference (Klein AM, Mazutis L, ... Kirschner MW).
- p. 9 Discussion
Klein et al. (Klein, 2015)
- p. 13 Reference list
Klein AM, Mazutis L, Akartuna I
- p. 13 Reference list
Cell PRESS. 2015
Judge's note: Page 9 and the reference entry on page 13 were checked. The paper elsewhere uses 'et al.' for multi-author works. 'Cell PRESS. 2015' signals in-press status and is not by itself an error.
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Typo "(log2(TPM+1) of the genes in each set": the outer parenthesis is never closed.
- p. 10 Methods, Cell cycle analysis
(log2(TPM+1) of the genes in each set
Judge's note: The page 10 crop shows the opening parenthesis before log2 with no matching close.
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Typo The Figure 2D legend heading reads "In silicoreconstruction" with no space.
- p. 17 Figure 2D legend heading
In silicoreconstruction of thousands of single-cell transcriptomes
Judge's note: The page 17 crop shows italic 'In silico' running directly into bold 'reconstruction'.
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Typo The Figure 3A,B legend has the misspellings "mixutres" (for mixtures) and "human-specifiic" (for human-specific).
- p. 18 Figure 3A,B legend heading
Drop-Seq analysis of mixutres of mouse and human cells
- p. 18 Figure 3A,B legend
human-specifiic
- p. 18 Figure 3 legend
mixutres
Judge's note: Both misspellings are visible in the page 18 image.
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Typo Figure 3A,B legend misspells 'human-specific' as "designated from these data as human-specifiic".
- p. 18 Figure 3A,B legend
designated from these data as human-specifiic
- p. 18 Figure 3 legend (A,B)
human-specifiic
Judge's note: The page image (crop and full p18) shows 'human-specifiic' in the typeset legend, so this is not an extraction artefact. The same legend also has 'mixutres' in its bold heading.
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Typo Figure 4C 'Novel, conserved cell cycle genes' lists the gene symbol "HISTH1E".
- p. 20 Figure 4C, novel conserved cell cycle genes
HISTH1E
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: the HGNC symbol for histone H1.4 at the time was HIST1H1E, and no symbol HISTH1E exists. On the p20 image the label clearly reads 'HISTH1E'. The authors should confirm the intended symbol.
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Typo Figure 6A legend prints the six gene symbols with no separators: "(Nrxn2Atp1b1Pax6Slc32a1Slc6a1Elavl3)".
- p. 24 Figure 6A legend
(Nrxn2Atp1b1Pax6Slc32a1Slc6a1Elavl3)
Judge's note: The crop image shows the typeset italic string with no commas or spaces between the symbols, so this is in the published text and not an extraction artefact.
Second check: none (judge only)