The Human Cell Atlas
2017 · paper · Biomedicine
Describes the Human Cell Atlas, an international effort to define all human cell types by their molecular profiles and link them to classical descriptions. It sets out the idea, potential uses, early proofs of concept, design considerations and a commitment to open data.
Checked: PDF from europepmc.org, fetched 4 Oct 2026. Page numbers are those of that PDF.
6 findings
Reference or label 'Rotem et al., 2015b' is cited in the list supporting 'various aspects of chromatin state', but its reference-list entry is 'High-throughput single-cell labeling (Hi-SCL) for RNA-seq using drop-based microfluidics', an RNA-seq method.
- p. 3 Introduction, second column
Rotem et al., 2015b
- p. 28 Reference list, Rotem 2015b
High-throughput single-cell labeling (Hi-SCL)
- p. 28 Reference list, Rotem 2015b
High-throughput single-cell labeling (Hi-SCL) for RNA-seq using drop-based microfluidics
- p. 3 Introduction, list of methods
various aspects of chromatin state
Only the authors can say what is right here.
Judge's note: Page 3 shows 'Rotem et al., 2015a; Rotem et al., 2015b' inside the chromatin-state citation group. The page 28 crop shows 2015a is the single-cell ChIP-seq paper and 2015b is the Hi-SCL RNA-seq paper. Box 1 cites only 2015a for chromatin, and the text search finds no other citation of 2015b. Judged from the reference list's own title; the authors may have meant it as the underlying droplet platform, so only they can say whether it belongs here.
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Reference or label 'Behjati et al., 2014' ('Genome sequencing of normal cells reveals developmental lineages and mutational processes') is cited among 'single-cell multi-omic methods to simultaneously measure several types of molecular profiles in the same cell'.
- p. 3 Introduction, second column, multi-omic list
Angermueller et al., 2016; Behjati et al., 2014;
- p. 22 Reference list, Behjati 2014
Genome sequencing of normal cells reveals
- p. 22 Reference list, Behjati 2014
Genome sequencing of normal cells reveals developmental lineages and mutation
- p. 3 Introduction, multi-omic methods
Behjati et al., 2014; Darmanis
Only the authors can say what is right here.
Judge's note: Page 3 shows Behjati 2014 in the multi-omic list, directly after being cited (appropriately) in the preceding list on DNA mutations and lineage reconstruction. The page 22 crop confirms the title is a genome-sequencing lineage study. The Box 1 multi-omics paragraph (pages 4-5) cites Angermueller, Dey, Macaulay, Albayrak, Darmanis, Frei and Genshaft, without Behjati. It was probably carried over from the previous citation group. Judged from the title in the reference list.
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Reference or label The reference list has two identical entries with different suffixes: 'Habib N, Li Y, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A. 2016a. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. Science 353:925–928' and the same entry as '2016b', with the same DOI (10.1126/science.aad7038) and PMID (27471252); the text cites both 'Habib et al., 2016a' and 'Habib et al., 2016b'.
- p. 24 Reference list, Habib 2016a
2016a. Div-Seq: Single-nucleus RNA-Seq reveals
- p. 24 Reference list, Habib 2016b
2016b. Div-Seq: Single-nucleus RNA-Seq reveals
- p. 4 Box 1, scRNA-seq paragraph
Habib et al., 2016b
- p. 4 Box 1, single-cell RNA-Seq paragraph
Habib et al., 2016b; Lake et al., 2016
Only the authors can say what is right here.
Judge's note: Viewed page 24: the two Habib entries are identical in authors, title, journal, volume, pages, DOI and PMID, and differ only in the a/b suffix. The text layer shows 'Habib et al., 2016b' in Box 1 (page 4, nuclei from frozen or lightly fixed tissue) and 'Habib et al., 2016a' elsewhere, including the Figure 3B credit. Either the entry was duplicated or a different Habib paper was meant for one of them; only the authors can say which, so this is an author query. Page 4 was checked in the text layer only.
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Reference or label Figure 3 legend says '(A) Myoblast differentiation in vitro', but panel A is titled 'Cell fate tracing (GPfates)', shows a bifurcation into branches labelled Th1 and Tfh, and is credited 'Figure 3A reprinted from Lönnberg et al., 2017'.
- p. 11 Figure 3 legend
(A) Myoblast differentiation in
- p. 11 Figure 3, panel A title and labels
Cell fate tracing (GPfates)
- p. 11 Figure 3 credit line
Figure 3A reprinted from Lönnberg et al., 2017 with permission.
- p. 11 Figure 3 caption
(A) Myoblast differentiation in vitro.
Judge's note: The page 11 image shows panel A with the title 'Cell fate tracing (GPfates)', a 'Bifurcation' marker and Th1 and Tfh branches. The legend describes (A) as myoblast differentiation in vitro, and the credit line gives Lönnberg et al., 2017, whose reference-list title is 'Temporal mixture modelling of single-cell RNA-seq data resolves a CD4+ T cell fate bifurcation'. The body text on the same page attributes myogenesis in vitro to Trapnell et al., 2014 and lists T helper cells with Lönnberg et al., 2017 among the bifurcated trajectories. No statement in the article explains the mismatch. The panel is T helper cell (Th1/Tfh) fate bifurcation, so the legend's description of panel A is wrong. The same legend also prints 'Gaussian process patent variable model', which looks like a slip for 'latent' (the panel axes are 'Latent variable 1/2'); that was not raised by the reviewers.
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Reference or label Figure 4 panel A is titled "Cell cycle in Th cells", but the legend describes it as "(A) The cell cycle in mouse hematopoietic stem and progenitor cells; adapted under terms of CC BY 4.0 from Scialdone et al. (2015)".
- p. 13 Figure 4, panel A title
Cell cycle in Th cells
- p. 13 Figure 4 legend
(A) The cell cycle in mouse hematopoietic stem and progenitor cells
- p. 13 Figure 4 legend (A)
The cell cycle in mouse hematopoietic stem and progenitor cells
- p. 13 Figure 4 caption (A)
The cell cycle in mouse hematopoietic stem and progenitor cells;
Only the authors can say what is right here.
Judge's note: Viewed page 13 and the legend crop: the title printed on panel A is "Cell cycle in Th cells" and the legend names mouse hematopoietic stem and progenitor cells. Elsewhere in the paper Th denotes T helper cells (Th1, Th17), which are not stem or progenitor cells, so the two labels name different populations. No statement in the text reconciles them. The reference-list entry for Scialdone et al. 2015 ("Computational assignment of cell-cycle stage from single-cell transcriptome data") does not say which cell type the panel shows, so only the authors can say which label is right.
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Wording "pioneering efforts for the brain and immune system in mouse (Bakken et al., 2016; Hawrylycz et al., 2012; Kim and Lanier, 2013; Miller et al., 2014) and for protein expression in human": the three brain references cited are, by their titles in the reference list, human or primate brain atlases, not mouse.
- p. 15 User's guide section, second column
neering efforts for the brain and immune system
- p. 24 Reference list, Hawrylycz 2012
anatomically comprehensive atlas of the adult human
- p. 26 Reference list, Miller 2014
Transcriptional landscape of the prenatal human
- p. 22 Reference list, Bakken 2016
primate brain development
Only the authors can say what is right here.
Judge's note: Viewed the page 15 crop and the three reference-list crops. Bakken 2016 is "A comprehensive transcriptional map of primate brain development", Hawrylycz 2012 is "An anatomically comprehensive atlas of the adult human brain transcriptome", and Miller 2014 is "Transcriptional landscape of the prenatal human brain". As printed, "in mouse" reads as covering both brain and immune system and is contrasted with "in human" in the next clause, so the wording misdescribes the cited brain work. "in mouse" may have been meant for the immune system only, or mouse brain atlas references may have been intended; the authors must say which. The Kim and Lanier entry was not opened.
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26 minor (typos and the like; most checked by the judge only)
Wording Figure 3 legend assigns "t-stochastic neighborhood embedding (B, D)" to panel B, but panel B's axes are labelled "biSNE 1" / "biSNE 2" (panel D: "tSNE 1" / "tSNE 2"); the legend never mentions biSNE. The method name is also written "t-stochastic neighborhood embedding" in the Figure 2 and Figure 3 legends, without "distributed".
- p. 11 Figure 3 legend
t-stochastic neighborhood embedding (B, D)
- p. 11 Figure 3, panel B axes
biSNE 1
- p. 9 Figure 2 legend
t-stochastic neighborhood embedding (A,B)
Judge's note: Viewed page 11 and the crops: panel B axes read biSNE 1/biSNE 2, panel D axes read tSNE 1/tSNE 2, and the legend groups B and D under t-stochastic neighborhood embedding. The label and legend do not match as printed. biSNE is a tSNE-based variant, so the legend may be a deliberate simplification; hence minor, and either form could be defended. The wording "t-stochastic neighborhood embedding" is printed on pages 9 and 11; that the standard name is "t-distributed stochastic neighbor embedding" is outside knowledge and is a cosmetic point only.
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Wording Figure 3B colour key lists overlapping time bins: "1–2 day", "3–4 day", "5–6 day", "6–7 day", "14 day"; day 6 falls in two bins.
- p. 11 Figure 3B legend
6–7 day
Judge's note: Viewed the crop of panel B: the key reads 1–2, 3–4, 5–6, 6–7 and 14 day, so the 5–6 and 6–7 bins overlap at day 6. Nothing in the legend or text explains the bins. The panel is reprinted from Habib et al., 2016a, and the bins may be carried over from that source as intended, so this is a consistency observation, not an established error. The source figure would settle it.
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Typo The same author is 'STEPHEN QUAKE' in the byline (p. 1) and 'Stephen Quake' in the author contributions (p. 21), but 'Steve Quake' in the affiliation list (p. 20).
- p. 1 Author list
STEPHEN QUAKE
- p. 20 Affiliation list
Steve Quake
Judge's note: Viewed the byline crop and the affiliation crop; both read as quoted. The contributions list in the text also has 'Stephen Quake'. This is an inconsistent name form in the article's own author metadata; either form is a legitimate name, so it is a consistency point and not an error of fact.
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Typo Number disagreement: 'manifest their action through impact in a particular cell types' (singular article with plural noun).
- p. 1 Introduction, second column
their action through impact in a particular cell
- p. 1 Introduction, final paragraph
through impact in a particular cell types
Judge's note: The page 1 crop shows 'in a particular cell' at the line end and 'types:' starting the next line. Should be 'a particular cell type' or 'particular cell types'.
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Typo Author's name misspelled in the text: "(Gary Nolan, unpublished results)" on page 14, against "GARRY NOLAN" in the byline and "Garry Nolan" in the affiliation list and contributions statement.
- p. 14 Disease section, first column
(Gary Nolan,
- p. 1 Author list
GARRY NOLAN
- p. 14 Disease section
Gary Nolan, unpublished results
Judge's note: Viewed the page 14 crop ("Gary Nolan, unpublished results"), the byline crop on page 1 ("GARRY NOLAN"), the affiliation list on page 20 ("Garry Nolan") and the contributions statement on page 21 ("Garry Nolan"). Three places spell it Garry; the in-text attribution alone has Gary.
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Typo Misspelling: 'trancriptome analysis by single cell RNA-Seq' should read 'transcriptome'.
- p. 3 Introduction, first column
trancriptome analysis by single cell RNA-Seq
Judge's note: The page 3 image, first column, shows 'trancriptome' as printed. Not an extraction artefact.
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Typo Box 1 reads 'Mass Ion Bean Imaging (Angelo et al., 2014)'; 'Bean' should be 'Beam', and the cited reference is titled 'Multiplexed ion beam imaging of human breast tumors'.
- p. 5 Box 1, in situ analysis paragraph
Mass Ion Bean Imaging (Angelo et al., 2014)
- p. 21 Reference list, Angelo et al. 2014
Multiplexed ion beam
- p. 5 Box 1, multiplex in situ analysis paragraph
Mass Ion Bean Imaging
- p. 3 Introduction
trancriptome analysis
Judge's note: The page 5 image shows 'Mass Ion Bean Imaging' as printed. The page 21 crop shows the Angelo et al. 2014 title 'Multiplexed ion beam imaging of human breast tumors', so 'Bean' is a misspelling, and 'Mass' also differs from the cited paper's name for the method ('Multiplexed'). One reviewer bundled 'trancriptome' and 'invglve' into this cluster; those are covered by C004 and C007 and are not counted again here.
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Typo Misspelling in Box 1: 'these methods invglve pre-defined signatures' should read 'involve'.
- p. 4 Box 1, mass cytometry paragraph
these methods invglve pre-defined signatures
Judge's note: The page 4 image shows 'invglve' in the mass cytometry paragraph as printed. Not an extraction artefact.
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Typo Subject-verb disagreement in Box 1: 'Power analyses provides a framework for comparing the sensitivity and accuracy of these approaches'.
- p. 4 Box 1, scRNA-seq paragraph
Power analyses provides a framework
Judge's note: The page 4 image shows the sentence as quoted. Should be 'Power analyses provide' or 'Power analysis provides'.
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Typo Misplaced parenthesis in Box 1: 'chromatin organization (by either single-cell ATAC-Seq; Buenrostro et al., 2015; Cusanovich et al., 2015) or single-cell ChIP-Seq (Rotem et al., 2015a), currently yield'.
- p. 4 Box 1, genome and epigenome paragraph
chromatin organization (by either
Judge's note: The page 4 image shows the text as quoted. The parenthesis opened before 'by either' closes after the first alternative, so the 'or' alternative falls outside it. Punctuation only; the meaning is recoverable.
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Typo Missing word: 'this 'living document', which will updated on a regular basis, was released on October 18, 2017' should read 'will be updated'.
- p. 5 Introduction, end
which will
- p. 5 Introduction, end
updated on a regular basis
- p. 5 Introduction, final paragraph
which will updated on a regular basis
Judge's note: The page 5 image, second column below Box 1, shows 'which will' at the line end followed by 'updated on a regular basis'. The word 'be' is missing.
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Typo Missing article: 'about an empire enamored with science of cartography' should read 'the science of cartography'.
- p. 6 First column
enamored with science of cartography
Judge's note: The page 6 crop shows the text as quoted, with no article before 'science'.
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Typo The italicised phrase 'expandio ad absurdum' is not a Latin form; a play on 'reductio ad absurdum' would be 'expansio ad absurdum'.
- p. 6 para on Borges
expandio ad absurdum
Judge's note: Rests on outside knowledge: that 'expandio' is not a Latin noun and that the noun from 'expandere' is 'expansio'. The page 6 crop shows 'expandio ad absurdum' in italics. In context (the map growing to the size of the empire) it is a deliberate play on 'reductio ad absurdum', so one reviewer's proposed fix to 'reductio' is wrong. Whether the authors intended 'expansio' or a free coinage is for them to say.
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Typo Garbled sentence on page 13: "because disease either elicits key perturbs cellular circuitry in informative ways"; "either" has no "or" and words are missing between "key" and "perturbs".
- p. 13 Disease section, second column
elicits key perturbs cellular circuitry
- p. 13 Disease: cells and cellular ecosystems, right column
because disease either elicits key perturbs cellular circuitry in informa-
- p. 13 Disease section
because disease either elicits key perturbs cellular circuitry
- p. 16 Sampling strategies
a smaller set of deep profiles can be help interpret
Judge's note: Viewed the crop of page 13, right column: the sentence is printed as quoted and does not parse. The exact intended wording (for example "either elicits key responses or perturbs") is for the authors, but the defect is plain. The cluster's other quotes are handled elsewhere: "can be help interpret" in C026 and "increasing tractable" in C029. "expandio ad absurdum" on page 6 is printed in italics and reads as a deliberate play on "reductio ad absurdum", so it is not confirmed as an error.
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Typo Figure 3 legend reads "Gaussian process patent variable model (A)"; "patent" should be "latent" (panel A's axes are labelled "Latent variable 1" and "Latent variable 2").
- p. 11 Figure 3 legend
patent variable model (A)
- p. 11 Figure 3, panel A axis
Latent variable 1
- p. 11 Figure 3 caption
Gaussian process patent variable model (A)
- p. 11 Figure 3 caption
Gaussian process
Judge's note: Viewed page 11 and the legend crop: the printed word is "patent". Panel A's own axis labels read "Latent variable 1/2", which shows the intended word inside the paper itself. Plain misspelling.
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Typo Figure 3 credit line has a stray second full stop: "© 2016 Macmillan Publishers Limited. . Figure 3C adapted from Haghverdi et al., 2016 with permission."
- p. 11 Figure 3 credit lines
Macmillan Publishers Limited. . Figure 3C
Judge's note: Viewed the crop and page 11: "Limited. . Figure 3C" is printed with two full stops, while the parallel Figure 3D line directly below has one.
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Typo Number disagreement: "and when T helper cell commit to their fate" should read "T helper cells commit".
- p. 12 Top of first column
when T helper cell commit
- p. 12
when T helper cell commit to their fate
Judge's note: Viewed the crop at the top of page 12: "when T helper cell commit to their fate (Lönnberg et al., 2017)" is printed. Singular noun with plural verb and plural "their".
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Typo Subject-verb disagreement: "the ratio of two processes may vary across cells, but are stable in each" should read "is stable".
- p. 12 Second column
cells, but are stable in each
Judge's note: Viewed the crop of page 12, second column: the text is printed as quoted. The subject is the singular "the ratio", so "are stable" does not agree.
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Typo "a future when the study of human biology and medicine is increasing tractable" should read "increasingly tractable".
- p. 19 Forward looking
medicine is increasing tractable
- p. 12 Development section
when T helper cell commit
- p. 16 Sampling strategies
can be help interpret
- p. 19 Forward looking
increasing tractable
Judge's note: Viewed the crop of page 19: "medicine is increasing tractable." is printed; an adverb is needed. The cluster's other two quotes ("when T helper cell commit", "can be help interpret") are also printed as quoted and are covered by C020 and C026.
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Typo The entry 'Scialdone A, Natarajan KN, Saraiva LR, Proserpio V, Teichmann SA, Stegle O, Marioni JC, Buettner F. 2015. Computational assignment of cell-cycle stage from single-cell transcriptome data' is out of alphabetical order, placed between 'Antebi YE' and 'Arthur G' on PDF page 22; separately, the Gaublomme 2015 title has a stray capital in 'Single-cell genomics Unveils critical regulators'.
- p. 22 Reference list, between Antebi and Arthur
Scialdone A, Natarajan KN, Saraiva LR, Proserpio V,
- p. 22 Reference list
Scialdone A, Theis FJ, Teichmann SA, Marioni JC,
- p. 13 Figure 4 caption
adapted under terms of CC BY 4.0 from Scialdone et al. (2015)
- p. 22 Reference list
Scialdone A, Natarajan KN, Saraiva LR
Judge's note: Viewed page 22: the Scialdone 2015 entry sits between Antebi and Arthur, while Scialdone 2016 is in the S section on page 28. The Figure 4 caption (page 13, text layer) cites 'Scialdone et al. (2015)', so a reader would look under S. Viewed page 24: 'Unveils' is capitalised mid-title in the Gaublomme entry. The claim that two references are both 'Scialdone et al., 2015' is a misreading: the second quoted entry is Buettner F, ..., Scialdone A, ... 2015, which is cited as Buettner et al., 2015, so the caption citation is not ambiguous. Confirmed for the ordering and capitalisation points only.
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Typo Extra word: "a smaller set of deep profiles can be help interpret the low-coverage data" should read "can help interpret".
- p. 16 Sampling strategies
deep profiles can be help
- p. 16 Sampling strategies, second paragraph
a smaller set of deep profiles can be help
- p. 16
a smaller set of deep profiles can be help interpret
Judge's note: Viewed the crop of page 16: "can be help interpret" is printed. Stray "be" (or missing "used to").
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Typo Apparent missing conjunction in "combine sound statistical sampling, biological enrichment purification, and insights from studies of model organisms" ("enrichment purification").
- p. 16 Sampling strategies
statistical sampling, biological enrichment purifi-
Only the authors can say what is right here.
Judge's note: Viewed the crop of page 16: the list is printed as quoted, with "enrichment purification" (hyphenated across a line break as "purifi-cation") and no "or", "and" or slash. It reads as two alternatives run together, but it could be meant as a compound noun, so this is a low-certainty cosmetic point for the authors.
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Typo Stray comma between subject and verb: "The full atlas, will ultimately describe at least 10 billion cells".
- p. 17 Biological scope
The full atlas, will ultimately describe
- p. 17 Biological scope, last paragraph
The full atlas, will ultimately describe at least
- p. 17 Biological scope
The full atlas, will ultimately describe at least 10 billion cells
Judge's note: Viewed the crop of page 17: the comma after "The full atlas" is printed and separates the subject from its verb.
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Typo Author's first name given two ways: "Stephen Quake" in the byline (page 1) and contributions statement (page 21), but "Steve Quake" in the affiliation list (page 20).
- p. 21
Ponting, Stephen Quake, Wolf Reik
Judge's note: Viewed the page 21 crop ("Ponting, Stephen Quake, Wolf Reik"), the byline crop on page 1 ("STEPHEN QUAKE") and the affiliation list on page 20 ("Steve Quake Department of Applied Physics and Department of Bioengineering"). The inconsistency is real, but Steve is a common short form of Stephen, so either could be legitimate; cosmetic only.
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Typo Three reference entries repeat an author under a variant spelling: Jojic 2013 'Jojic V, Shay T, ... Regev A, Koller D, Best AJ, Knell J, Goldrath A, Joic V, Koller D, Shay T, Regev A, Cohen N' (Jojic as 'Joic', with Koller, Shay and Regev each listed twice); Kim JK 2015 'Ilicic T, Illicic T'; Ramilowski 2015 'Kloppmann E, Kloppman E'.
- p. 25 Reference list, Jojic 2013
Goldrath A, Joic V, Koller
- p. 25 Jojic et al. 2013
Joic V, Koller
- p. 25 Kim et al. 2015
Ilicic T, Illicic T
- p. 27 Ramilowski et al. 2015
Kloppmann E, Kloppman E
Judge's note: Viewed pages 25 and 27: all three strings are printed as quoted. In the Jojic entry the first author reappears as 'Joic V' and Koller D, Shay T and Regev A each appear twice. The adjacent near-identical surnames with the same initial in the Kim and Ramilowski entries are duplicates with a spelling variant. Which spelling is right in the Kim and Ramilowski entries cannot be told from the page, but the duplication itself is evident.
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Typo The Shapiro 2010 reference has a misplaced comma in the access date: '[Accessed 28, November 2017]'.
- p. 28 Shapiro 2010 reference
[Accessed 28, November 2017]
Judge's note: Viewed page 28: the entry reads 'Shapiro E. 2010. The human cell lineage flagship initiative. http://www.lineage-flagship.eu/ [Accessed 28, November 2017].' The comma after the day is in the printed page, across a line break, and is not an extraction artefact. This is the only 'Accessed' date in the text layer, so there is no house pattern to compare it with.
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