Mapping and Quantifying Mammalian Transcriptomes by RNA-Seq
Nature Methods, 2008 · paper · Biomedicine
Studies mapping and quantifying mammalian transcriptomes by RNA sequencing. The text provided is supplementary material, covering RNA fragmentation, read uniformity, reads mapping to multiple places, and expression values for mouse brain, liver and muscle.
Checked: PDF from media.springernature.com, fetched 4 Oct 2026. Page numbers are those of that PDF.
4 findings
Substance Supp Fig 2 Venn: the Muscle circle is labelled '(6219)', but its regions 957+810+4019+432 sum to 6218; the Brain (8884), Liver (6293) and '11071 Total' labels all match their regions.
- p. 4 Supplementary Figure 2 Venn diagram, Muscle label
Muscle (6219)
Only the authors can say what is right here.
Judge's note: Read the p4 image; all digits are clear. Integer gene counts, so rounding cannot explain the gap. Nothing in the files explains the off-by-one. Because the other labels and the union reconcile, the Muscle label is the likely error, but only the authors can confirm.
Second check: another model agreed
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Substance Supp Fig 6 Venn: '241 Total', but the seven regions (109, 16, 41, 30, 6, 8, 33) sum to 243; the circle totals 161, 95 and 77 all reconcile with their regions.
- p. 8 Supplementary Figure 6 Venn diagram
241 Total
Judge's note: Read the p8 image; the digits are clear. Integer counts, and no exclusion is stated anywhere.
Second check: another model agreed
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Substance Supp Table 1, Brain (spiked) row '54.3% 3.3% 10.6% 1.6% 0.1% 25% 73.4%': Used is defined as '(= unique + splices + multi (2-10))', which gives 68.2% (68.3% with spikes), not 73.4%; the row categories sum to 94.9%.
- p. 9 Supplementary Table 1, Brain (spiked) row
73.4%
- p. 9 Supplementary Table 1 footer
(= unique + splices + multi (2-10))
- p. 9 Supplementary Table 1, Brain (spiked)
54.3% 3.3% 10.6% 1.6% 0.1% 25% 73.4%
Only the authors can say what is right here.
Judge's note: Read the p9 image. Every other row sums to about 100% (99.5–100.1). Used = 100 − No Match − Multi(11+) = 73.4, and the Used × Total figures sum to about 140M, matching the footer 'used 140 M total reads'. This suggests a component (e.g. Uniques) is misprinted, but only the authors can say which.
Second check: another model agreed
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Substance Supplementary Methods: 'For the long category (1500 nt), two fragments of the phage lambda...' contradicts the length classes defined in the same paragraph ('~ 300 nt, ~1500 nt, and ~10,000 nt'), where 1500 nt is the intermediate class.
- p. 13 Supplementary Methods, Spike controls derivation and validation
For the long category (1500 nt)
- p. 13 Supplementary Methods, Spike controls derivation and validation
For the long category (1500 nt), two fragments of the phage lambda
- p. 13 Spike controls derivation and validation
(~ 300 nt, ~1500 nt, and ~10,000 nt)
Judge's note: Seen on p13. The same paragraph assigns '(1500 nt)' to the intermediate category, so the long category should be ~10,000 nt.
Second check: another model agreed
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12 minor (typos and the like; most checked by the judge only)
Wording Supp Fig 6: the text says '596 RNAFAR consolidated regions ... were called, with 368 higher than 5 RPKM in one or more tissues', while the Venn of 'RNAFAR regions that have an RPKM greater than 5.0' totals 241 (243 by summation).
- p. 8 Supplementary Figure 6 text below diagram
with 368 higher than 5 RPKM in one or more tissues
- p. 8 Supplementary Figure 6 Venn diagram
241 Total
Only the authors can say what is right here.
Judge's note: Seen on p8. The caption and the sentence appear to describe the same set and threshold, and nothing in the files reconciles 368 with 241/243. The Venn may use a different filter, so this is a query to the authors about which set each number counts.
Second check: another model agreed
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Wording Supp Table 1, Brain row '50.3% 3.1% 9.7% 1.7% 0 34.7% 63.5%': unique + splices + multi(2-10) = 63.1%, not 63.5%, and the row sums to 99.5%.
- p. 9 Supplementary Table 1, Brain row
63.5%
- p. 9 Supplementary Table 1, Brain
50.3% 3.1% 9.7% 1.7% 0 34.7% 63.5%
Only the authors can say what is right here.
Judge's note: Read the p9 image. The gaps (0.4 and 0.5 points) are small but larger than rounding of one-decimal entries would normally give; the other unspiked rows reconcile to within 0.1.
Second check: another model agreed
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Wording Supp Table 1: in the Liver (spiked) and Muscle (spiked) rows, Used (60%, 65.1%) matches unique + splices + multi(2-10) only if spike reads are added, although the footer defines Used as '(= unique + splices + multi (2-10))'.
- p. 9 Supplementary Table 1, Liver (spiked) and Muscle (spiked) rows
65.1%
Judge's note: Read the p9 image. Without spikes: Liver 59.1, Muscle 63.4. With spikes: 60.1 and 65.0. Whether spike reads count as 'used' is not stated, so the definition is ambiguous.
Second check: another model agreed
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Typo Contents list wording differs from item titles: 'RNAFAR regions at the 3' end of Mef2D' vs Supp Fig 5 title 'RNAFAR region...'; 'new transcript in liver' vs Supp Table 4 title 'new transcripts in liver'; Supp Table 2 entry omits 'regions' after 'intergenic'.
- p. 1 Contents list
RNAFAR regions at the 3' end of Mef2D
- p. 12 Supp Table 4
new transcripts in liver
Judge's note: Checked p1 contents list against the p7 Supp Fig 5 title and the p12 Supp Table 4 title; the text layer shows that the Supp Table 2 title reads 'intergenic regions'. The differences are cosmetic.
Second check: none (judge only)
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Typo Gene symbol capitalised three ways: 'Mef2D' (Supp Fig 5 title and contents), 'Mef2d' (panel title and legend) and 'mef2d' ('the 3’UTR for mef2d in muscle').
- p. 7 Supplementary Figure 5 title and caption
RNAFAR region at the 3’ end of Mef2D.
- p. 7 Supplementary Figure 5 caption
the 3’UTR for mef2d in muscle
- p. 1 Contents list
RNAFAR regions at the 3' end of Mef2D.
- p. 7 Supp Fig 5 legend
3’ end of Mef2d
Judge's note: Seen on p1 and p7. Cosmetic inconsistency; the meaning is unaffected.
Second check: none (judge only)
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Typo Supp Fig 1 legend spells the test 'Kolmogorov/Smirnoff (KS) statistic'; the standard name is Kolmogorov–Smirnov.
- p. 2 Supplementary Figure 1 caption
Kolmogorov/Smirnoff (KS) statistic
Judge's note: Seen on p2. 'Smirnoff' is an occasional transliteration, so this is cosmetic.
Second check: none (judge only)
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Typo Supp Fig 1C legend: '(muscle = red. liver = black)' has a full stop where a comma or semicolon belongs.
- p. 2 Supp Fig 1C
muscle = red. liver = black
Judge's note: Seen at the bottom of p2. Punctuation only.
Second check: none (judge only)
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Typo Supp Fig 3 legend: 'mouse genome and muscle transcriptiome' misspells 'transcriptome' (the panel title reads 'Muscle transcriptome').
- p. 5 Supplementary Figure 3 caption
muscle transcriptiome
- p. 5
mouse genome and muscle transcriptiome
Judge's note: Seen on p5.
Second check: none (judge only)
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Typo Supp Fig 5 legend: 'AK007191/AK00852' drops a digit; the figure track label reads 'AK008852'.
- p. 7 Supplementary Figure 5 caption
AK007191/AK00852
- p. 5 Supp Fig 3 legend
muscle transcriptiome
Judge's note: Seen on p7: the legend prints AK00852 and the figure prints AK008852. The second crop (the 'transcriptiome' typo) is covered by C005.
Second check: none (judge only)
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Typo Supplementary Methods: 'prior to use in .the Illumina Cluster generation protocol' has a stray period before 'the'.
- p. 13 Supplementary Methods, Adapter ligation paragraph
prior to use in .the Illumina Cluster generation protocol
- p. 13 Adapter ligation paragraph
prior to use in .the Illumina Cluster
Judge's note: The stray period is visible on the p13 image.
Second check: none (judge only)
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Typo Supplementary Methods, Sequencing paragraph: the unit is printed in capitals in "32BP versus 25BP" and "uniquely mappable at 32 BP", but as "bp" everywhere else in the same paragraph ("25bp", "4 bp", "32 bp reads").
- p. 13 Sequencing paragraph
32BP versus 25BP
Judge's note: I opened the crop. On p.13 the same paragraph uses "25bp", "4 bp", "1 or 2 bp", "25 bp" and "32 bp", alongside "32BP versus 25BP" and "32 BP". This is a cosmetic inconsistency in how the unit is written. The meaning is clear either way.
Second check: none (judge only)
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Typo Supplementary Methods, background paragraph: "background RPKM is 5.32 * 10-17". The exponent sits on the baseline at full size, so read literally it is 10 minus 17 rather than 10^-17.
- p. 14 Supplementary Methods, background paragraph
5.32 * 10-17
Judge's note: I opened the crop of p.14. The rendered text shows "5.32 * 10-17" inline at normal size, with no superscript, so this is not an extraction artefact. From the context (a binomial tail probability), the intended value is clearly 5.32 × 10^-17, so this is a typesetting slip. I also checked the expected read counts in the same paragraph: 0.05 RPKM × 2 kb × 40M reads = 4 reads, and 1 RPKM gives 80 reads. Both match the printed values.
Second check: none (judge only)