Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells
2014 · paper · Biomedicine
Presents a lentiviral library of 64,751 guide sequences targeting 18,080 genes for genome-scale CRISPR-Cas9 knockout screens in human cells. It identified essential genes and genes whose loss confers resistance to vemurafenib in melanoma cells, including novel hits.
0 findings
None that passed a second check.
13 minor (typos and the like; most checked by the judge only)
Wording The text says "all 5 sgRNAs showed >99% allele modification 14 days post-transduction (Fig. 4C)", but Fig. 4C has a bar for sgRNA 5 only under the "14 day" bracket.
- p. 3 Main text, validation paragraph
all 5 sgRNAs showed >99% allele modification 14 days post-transduction (Fig. 4C)
- p. 9 Fig. 4C
14 day
- p. 9 Fig. 4C panel (x-axis labels under "7 day" and "14 day" brackets)
7 day
Only the authors can say what is right here.
Judge's note: Fig. 4 is on PDF page 10, not page 9 (page 9 holds Fig. 3). The Fig. 4C panel shows bars for sgRNAs 1-5 under '7 day' (four near 100%, sgRNA 5 about 65%) and a single bar, labelled 5, under '14 day'. The cited panel therefore shows no day-14 values for sgRNAs 1-4. Those data may exist elsewhere, but the figure cited does not show them. Only the authors can say.
Second check: another model agreed
Report a problem with this finding
Wording The text says "only the best shRNA achieved sufficient knockdown to increase PLX resistance (Fig. 4E)", while the Fig. 4E legend says cells with NF2-targeting shRNA vectors show no significant EC50 increase ("F1,8 = 0.47, p = 0.51").
- p. 3 Results, last paragraph
only the best shRNA achieved sufficient knockdown to increase PLX resistance (Fig. 4E)
- p. 10 Fig. 4 legend, panel E
whereas cells transduced with NF2-targeting shRNA vectors do not (F1,8 = 0.47, p = 0.51, n = 4 replicates)
- p. 3 Results, validation paragraph
only the best shRNA achieved sufficient knockdown to increase PLX resistance
- p. 10 Fig. 4 legend
targeting shRNA vectors do not (F1,8 = 0.47, p = 0.51
Only the authors can say what is right here.
Judge's note: In the Fig. 4E right-hand panel on page 10, the NF2_sh1 points sit somewhat above the common curve, but no separate fitted curve is shown. The legend reports one non-significant test for the shRNA vectors. The paper does not say which shRNA is 'the best' or how that claim relates to the reported test, which appears to be a pooled one. This is a query, not a statement that either reading is wrong.
Second check: another model agreed
Report a problem with this finding
Typo Affiliation 1 reads "Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA" (no city), while affiliation 3 gives the same address as "Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA".
- p. 1 Affiliation 1
Broad Institute of MIT and Harvard, 7 Cambridge Center, MA 02142, USA
- p. 1 Affiliation 3
7 Cambridge Center, Cambridge, MA 02142, USA
- p. 1 Affiliation 3
Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, 7 Cambridge Center, Cambridge, MA 02142, USA
Judge's note: Page 1 image: affiliation 1 has no city between 'Cambridge Center' (a street) and 'MA'; affiliation 3 has the same street and ZIP code with 'Cambridge,' and gives the institute name in the opposite order. This is a cosmetic inconsistency in the front matter.
Second check: none (judge only)
Report a problem with this finding
Typo The byline prints the author's surname as "Tarjei Mikkelson"; the usual spelling of his name is Mikkelsen.
- p. 1 Author list
Tarjei Mikkelson
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: that the author's surname is spelled 'Mikkelsen'. The page 1 image shows 'Mikkelson'. The name appears nowhere else in the files, so the files cannot settle the spelling.
Second check: none (judge only)
Report a problem with this finding
Typo The CRISPR acronym is expanded as "clustered regularly interspaced short palindrome repeats" instead of "... short palindromic repeats".
- p. 2 Introduction, second paragraph
CRISPR (clustered regularly interspaced short palindrome repeats)
- p. 2 Introduction
short palindrome repeats
Only the authors can say what is right here.
Judge's note: Rests on outside knowledge: the standard expansion of CRISPR uses 'palindromic'. The page 2 image shows 'short palindrome repeats'.
Second check: none (judge only)
Report a problem with this finding
Typo The Fig. 2 legend abbreviates the method as "Gene Set Enrichment Analysis (DSEA) (15)", whereas the main text defines it as "(GSEA) (15)".
- p. 8 Fig. 2 legend (D and E)
indentified by Gene Set Enrichment Analysis (DSEA) (15)
- p. 2 Main text
Gene set enrichment analysis (GSEA) (15)
- p. 8 Fig. 2 legend
Gene Set Enrichment Analysis (DSEA)
- p. 8 Fig. 2 legend (D and E)
Gene Set Enrichment Analysis (DSEA) (15)
Judge's note: The page 8 image shows '(DSEA)'. On page 2 the main text has 'Gene set enrichment analysis (GSEA) (15)'. Both cite the same reference, so DSEA is a typo for GSEA.
Second check: none (judge only)
Report a problem with this finding
Typo The acknowledgments stop mid-name: "... Simons Foundations, Bob Metcalfe, and Jane", with no surname and no full stop.
- p. 4 Acknowledgments
Simons Foundations, Bob Metcalfe, and Jane
- p. 4 Acknowledgments, final line
Bob Metcalfe, and Jane
Judge's note: The page 4 image shows the paragraph ending at 'and Jane', with the 'References and Notes' heading directly below.
Second check: none (judge only)
Report a problem with this finding
Typo The Fig. 1A legend reads "Puromycin selection rev marker (puro), psi packaging signal (psi+), response element (RRE)". The italic 'rev' belongs before 'response element (RRE)'.
- p. 7 Fig. 1 legend (A)
Puromycin selection rev marker (puro), psi packaging signal (psi+), response element (RRE)
Judge's note: The page 7 image shows italic 'rev' between 'selection' and 'marker' in the typeset legend, so this is not an extraction artefact.
Second check: none (judge only)
Report a problem with this finding
Typo The Fig. 2 legend misspells 'identified' as "indentified by Gene Set Enrichment Analysis".
- p. 8 Fig. 2 legend (D and E)
indentified by Gene Set Enrichment Analysis
- p. 8 Fig. 2 legend D and E
indentified
- p. 8 Fig. 2 legend
indentified by Gene Set Enrichment
- p. 8 Fig. 2 legend
indentified by Gene Set
Judge's note: The misspelling is visible in the page 8 image of the legend.
Second check: none (judge only)
Report a problem with this finding
Typo The Fig. 2 legend (D and E) has "A375 cells p < 10−5, FDR-corrected q < 10−5)", with a closing parenthesis but no opening one, and lacks the 'nominal' qualifier used in the parallel HUES62 clause "(nominal p < 10−5".
- p. 8 Fig. 2 legend (D and E)
A375 cells p < 10−5, FDR-corrected q < 10−5) and HUES62 cells (nominal p < 10−5
- p. 8 Fig. 2 legend, panels D and E
in A375 cells p < 10−5, FDR-corrected q < 10−5) and HUES62 cells (nominal p < 10−5
- p. 8 Fig. 2 legend
A375 cells p < 10−5, FDR-
- p. 8 Fig. 2 legend (D and E)
A375 cells p < 10−5, FDR-corrected q < 10−5)
Judge's note: The page 8 image shows no '(' before 'p' in the A375 clause but a ')' after 'q < 10−5'. The HUES62 clause opens with '(nominal'. The difference in q thresholds (10−5 vs 10−3) concerns two different cell lines and is not treated as a defect.
Second check: none (judge only)
Report a problem with this finding
Typo The Fig. 2A legend has a missing space: "Design ofsgRNA library".
- p. 8 Fig. 2 legend (A)
Design ofsgRNA library
- p. 8 Fig. 2 legend, panel A
Design ofsgRNA library for genome-scale knockout
Judge's note: The page 8 image shows 'ofsgRNA' set without a word space.
Second check: none (judge only)
Report a problem with this finding
Typo The Fig. 4A legend misspells 'Redundant' in the RSA expansion: "Redudant siRNA Activity (RSA)".
- p. 10 Fig. 4 legend (A)
Redudant siRNA Activity (RSA)
- p. 10 Fig. 4 legend, panel A
Analysis using the Redudant siRNA Activity (RSA) algorithm
Judge's note: The misspelling is visible in the page 10 image of the legend.
Second check: none (judge only)
Report a problem with this finding
Typo The panel label in the Fig. 4 legend has no closing parenthesis: "(A RIGER p values for the top 100 hits", whereas the other panels read (B), (C), and so on.
- p. 10 Fig. 4 legend (A)
(A RIGER p values for the top 100 hits
- p. 10 Fig. 4 legend
(A RIGER p values
Judge's note: The page 10 image shows '(A RIGER' with no ')'.
Second check: none (judge only)