Claims 33
From the paper Cell Atlas and Novel Signal Processing Strategy in Primate Insular Cortex · claims file · checked 2026-10-21: ready
- fig5b-sepsc-frequency
The frequency of spontaneous EPSCs is lower in VENs than in neighbouring PCs.
The frequencies of both excitatory and inhibitory events were significantly lower in VENs than in PCs (Fig. 5b )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5bHow it will be judged
Per cell, sEPSCs are detected in the recording held at -70 mV (inward events), and the cell's frequency is the number of events over the duration analysed, in Hz (Methods, "Recordings of synaptic events were assessed for frequency (Hz)"; the code's tables give one frequency per cell as events over duration). The Methods fix the event threshold at "the maximus root mean squared noise level (5 pA)" and give no other detection parameter (miniAnalysis settings such as baseline window or area threshold are not given, and the code holds no detection step); a standard peak detector on the baseline-subtracted trace is used, and the threshold has two readings, (a) a fixed 5 pA amplitude and (b) the recording's own RMS noise level. The peak detector itself is a standard choice, not the paper's (miniAnalysis is not reproduced). The Methods say each trace was recorded for at least 5 min after the signal had stabilized (no shift beyond 4 s.d. of the baseline) and that at least 200 events were included for analysis, but not how long a stretch was analysed; the analysis uses the whole stable recording, and the code's 30 s per cell (its mIPSC table) is shown as a variant. Cell types are the dataset's labels; the paper's n is 8 VENs and 11 PCs (Fig. 5b legend), of which the code's 11 PCs are 10 distinct cells (one cell's two traces counted twice), so the PC group is read (a) as the paper's 11 entries and (b) as 10 distinct cells. Test, as in the legend and in Fig5ab_ana_sPSC.m, a two-tailed Wilcoxon rank-sum test of VEN against PC per-cell frequencies, uncorrected, at p < 0.05 (conventional; the panel's p-value was not readable). Reproduced when, under every combination of the readings, the VEN median is below the PC median with p < 0.05; blocked as methods_underspecified when the readings disagree, with every result shown. Group medians and ranges are reported.
- fig5b-sipsc-frequency
The frequency of spontaneous IPSCs is lower in VENs than in neighbouring PCs.
The frequencies of both excitatory and inhibitory events were significantly lower in VENs than in PCs (Fig. 5b )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5bHow it will be judged
As fig5b-sepsc-frequency, for sIPSCs, with n = 7 VENs and 8 PCs (Fig. 5b legend) and no duplicate reading. The Methods hold IPSCs at -60 mV with a CsCl internal (inward events); the code's metadata names the sIPSC recordings "+20mV", which would make the events outward. Events are detected in the direction implied by the holding potential the file records, and the notebook says which it is. Threshold readings (a) 5 pA and (b) the recording's RMS noise; whole stable recording, with the code's 30 s as a variant. Two-tailed Wilcoxon rank-sum, uncorrected, p < 0.05 (conventional). Reproduced when both readings give the VEN median below the PC median with p < 0.05; blocked as methods_underspecified when they disagree.
- fig5b-mepsc-frequency
The frequency of miniature EPSCs (in tetrodotoxin) is lower in VENs than in neighbouring PCs.
The frequencies of both excitatory and inhibitory events were significantly lower in VENs than in PCs (Fig. 5b )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5bHow it will be judged
As fig5b-sepsc-frequency, for mEPSCs held at -70 mV in 1 uM tetrodotoxin, with n = 8 VENs and 8 PCs (Fig. 5b legend). Threshold readings (a) 5 pA and (b) the recording's RMS noise; whole stable recording, with the code's 30 s as a variant. Two-tailed Wilcoxon rank-sum, uncorrected, p < 0.05 (conventional), as in Fig5ab_ana_mPSC.m. Reproduced when both readings give the VEN median below the PC median with p < 0.05; blocked as methods_underspecified when they disagree. The test uses the dataset's cell-type labels. The paper's analysis sheet labels these cells the other way from the code's deposit metadata (see the opening comment), so the notebook also reports the result with each cell's label taken from the sheet (matched through the original file names in metadata_PSC.csv), as a variant that does not decide the outcome, and records which labelling the dataset carries.
- fig5b-mipsc-frequency
The frequency of miniature IPSCs (in tetrodotoxin) is lower in VENs than in neighbouring PCs.
The frequencies of both excitatory and inhibitory events were significantly lower in VENs than in PCs (Fig. 5b )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5bHow it will be judged
As fig5b-sipsc-frequency, for mIPSCs in 1 uM tetrodotoxin, with n = 15 VENs and 21 PCs (Fig. 5b legend). Threshold readings (a) 5 pA and (b) the recording's RMS noise; the duration analysed follows the Methods (whole stable recording); the code's mIPSC table counts events over 30 s per cell, and that is shown as a variant. Two-tailed Wilcoxon rank-sum, uncorrected, p < 0.05 (conventional). Reproduced when both readings give the VEN median below the PC median with p < 0.05; blocked as methods_underspecified when they disagree.
- fig5c-sepsc-amplitude
The amplitude of spontaneous EPSCs does not differ significantly between VENs and PCs.
whereas the amplitudes were not significantly different between VENs and PCs (Fig. 5c )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5cHow it will be judged
A claim of absence, judged on the paper's test, a two-tailed Wilcoxon rank-sum test of VEN against PC per-cell amplitudes (Fig. 5c legend; Fig5ab_ana_sPSC.m), uncorrected, at alpha 0.05 (conventional). The cell's amplitude is the mean amplitude of its detected events, in pA (the code's tables give an average amplitude per cell). Events are detected as for fig5b-sepsc-frequency, with the 5 pA threshold the Methods print, over the whole stable recording, on the paper's 8 VENs and 11 PC entries. Reproduced when p >= 0.05, not reproduced when p < 0.05; the medians, their difference and p are reported either way, and the RMS-noise threshold, the 10 distinct PCs and the 30 s window are shown as variants.
- fig5c-sipsc-amplitude
The amplitude of spontaneous IPSCs does not differ significantly between VENs and PCs.
whereas the amplitudes were not significantly different between VENs and PCs (Fig. 5c )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5cHow it will be judged
As fig5c-sepsc-amplitude, for sIPSCs (7 VENs, 8 PCs), with events detected as for fig5b-sipsc-frequency. Reproduced when the two-tailed Wilcoxon rank-sum test gives p >= 0.05, not reproduced when p < 0.05; effect size reported either way.
- fig5c-mepsc-amplitude
The amplitude of miniature EPSCs does not differ significantly between VENs and PCs.
whereas the amplitudes were not significantly different between VENs and PCs (Fig. 5c )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5cHow it will be judged
As fig5c-sepsc-amplitude, for mEPSCs (8 VENs, 8 PCs), using the dataset's cell-type labels, with the sheet's labelling shown as a variant (see fig5b-mepsc-frequency). Reproduced when the two-tailed Wilcoxon rank-sum test gives p >= 0.05, not reproduced when p < 0.05; effect size reported either way.
- fig5c-mipsc-amplitude
The amplitude of miniature IPSCs does not differ significantly between VENs and PCs.
whereas the amplitudes were not significantly different between VENs and PCs (Fig. 5c )
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 1; Figure 5cHow it will be judged
As fig5c-sepsc-amplitude, for mIPSCs (15 VENs, 21 PCs), with events detected as for fig5b-mipsc-frequency. Reproduced when the two-tailed Wilcoxon rank-sum test gives p >= 0.05, not reproduced when p < 0.05; effect size reported either way.
- scrna-classes
The whole-cell scRNA-seq atlas of the macaque AIC holds 122,663 transcriptomes in four classes, excitatory neurons (21,733, 17.8%), inhibitory neurons (17,007, 13.9%), glial cells (83,283, 67.8%) and vascular cells (640, 0.5%).
we categorized these cells into four main classes: excitatory neurons (21,733 cells, 17.8%), inhibitory neurons (17,007 cells, 13.9%), glial cells (83,283 cells, 67.8%) and vascular cells (640 cells, 0.5%)
Results, Transcriptomic landscape of the macaque AIC, paragraph 2; Figure 1b,c - scrna-78-types
The four classes divide into 20 subclasses and 78 transcriptomic types, 34 inhibitory, 20 excitatory and 24 non-neuronal.
The four classes were divided into 20 subclasses and further subdivided into 78 molecularly defined transcriptomic cell types, including 34 inhibitory and 20 excitatory neuron types, and 24 non-neuronal cell types
Results, Transcriptomic landscape of the macaque AIC, paragraph 2; Extended Data Figure 1e,fHow it will be judged
Judged on the paper's cluster labels if the deposit carries them (counts of types per class equal to those stated); a re-clustering with the Methods' pipeline (SCANPY, Harmony, Leiden) has no stated resolution, so the number of clusters it gives cannot decide the claim.
- scrna-no-sex-difference
No significant sex differences were found in the representation of cell types.
No significant sex differences were observed in cell types (Supplementary Fig. 3 )
Results, Transcriptomic landscape of the macaque AIC, paragraph 2; Supplementary Figure 3How it will be judged
A claim of absence. The test is shown in Supplementary Fig. 3, which was not in the text read, so the paper's test and threshold are not known here; blocked as methods_underspecified unless they are supplied.
- patchseq-mapping
Of 307 Patch-seq neurons with transcriptomes, 273 excitatory neurons map to 18 of the 20 excitatory types and 34 inhibitory neurons to 17 of the 33 inhibitory types.
273 excitatory neurons mapped to 18 of the 20 excitatory types, while 34 inhibitory neurons mapped to 17 of the 33 inhibitory types
Results, Patch-seq revealed extensive cellular heterogeneity in the primate AIC, paragraph 1; Figure 1e - ven-map-et-ct
The 29 morphologically identified VENs do not map to one molecular cluster; 14 map to L5 ET and 15 to L5/6 CT.
29 neurons that were morphologically identified as VENs did not map to a unique molecular cluster; instead, they mapped to either L5 ET ( n = 14) or L5/6 CT ( n = 15)
Results, Patch-seq revealed extensive cellular heterogeneity in the primate AIC, paragraph 2; Figure 2a - fig2d-f-l23-it-tau-width
Among projection neuron subclasses, L2/3 IT HPCAL1 neurons have a small membrane time constant and a narrow AP width.
L2/3 IT HPCAL1 neurons stood out with a small membrane time constant (tau) and narrow action potential (AP) width (Fig. 2d–f )
Results, Patch-seq revealed extensive cellular heterogeneity in the primate AIC, paragraph 3; Figure 2d-fHow it will be judged
Per cell, tau and AP half-width as defined in the Methods (Extraction of electrophysiological features). Two-tailed Wilcoxon rank-sum tests between subclasses with Benjamini-Hochberg FDR correction (Fig. 2 legend), n as in the legend (L2/3 IT HPCAL1 30, IT RORB 17, L5 IT FEZF2 119, VEN 22, L5 ET 16, L6 PC 13; the Results give L6 PC n = 14). The paper says only that the subclass "stood out", and its adjusted p-values are in Supplementary Table 2, not read, so how many pairwise differences must be significant is open. Readings, (a) the lowest median tau and the lowest median AP width of the six subclasses, each lower than every other subclass at FDR-adjusted p < 0.05 (conventional), and (b) the lowest median of each of the two, without a requirement on the pairwise tests. Reproduced when both readings hold; blocked as methods_underspecified when they disagree.
- ven-firing-rate-variability
VENs have lower firing rates and greater variability in spike timing than PCs.
Notably, VENs exhibit lower firing rate and greater variability in spike timing than PCs
Results, Patch-seq revealed extensive cellular heterogeneity in the primate AIC, paragraph 3; Supplementary Tables 1 and 2How it will be judged
The paper's values and tests are in Supplementary Tables 1 and 2, not in the text read, and the measure of spike-timing variability is not named in the text; blocked as methods_underspecified unless they are supplied.
- fig3c-ais-distance-length
In Pan-Nav stained sections the AIS of VENs lies farther from the soma than that of PCs, and VENs have a shorter AIS.
showed that the AIS in VENs was, on average, located significantly farther from the soma than in PCs (Fig. 3c ). Additionally, VENs had a shorter AIS than PCs.
Results, The AIC evolved a neural signal-processing strategy, paragraph 2; Figure 3cHow it will be judged
The legend names a two-way ANOVA (n = 108 VENs and 430 PCs, 23 slices, five animals) without its factors; the readings are cell type with slice, and cell type with animal, as the second factor. Reproduced when, under both, the cell-type effect is significant at p < 0.05 (conventional) for AIS distance (VEN larger) and AIS length (VEN shorter).
- fig3e-phase-peak-index
VENs have lower AP phase-plane peak indices than every PC type.
The VENs had lower phase peak indices than any type of PCs (Fig. 3e )
Results, The AIC evolved a neural signal-processing strategy, paragraph 3; Figure 3eHow it will be judged
Phase peak index (Psd - Pais)/(Psd + Pais) from the phase-plane of the AP (Methods, Calculation of the phase peak index). Kruskal-Wallis test followed by Dunn's test (Fig. 3e legend), cells as in Fig. 2d-f. Reproduced when the VEN median is the lowest and Dunn's test separates VENs from each PC type at p < 0.05 (conventional).
- fig4ac-ap-width-amplitude
In 281 VENs and 306 L5 PCs, APs of VENs are broader and lower in amplitude.
APs in VENs were broader and had a lower amplitude compared with L5 PCs (Fig. 4a-c )
Results, The AIC evolved a neural signal-processing strategy, paragraph 3; Figure 4a-cHow it will be judged
AP amplitude and half-width of the first AP as in the Methods. Reproduced when VEN median width is larger and amplitude smaller, each with two-tailed Wilcoxon rank-sum p < 0.001.
- fig4d-sodium-current
Somatic Na+ currents in outside-out patches are lower in VENs (n = 14) than in L5 PCs (n = 21).
outside-out patch-clamp recording showed that the somatic Na + currents evoked in VENs ( n = 14) were significantly lower than those of L5 PCs ( n = 21) (Fig. 4d )
Results, The AIC evolved a neural signal-processing strategy, paragraph 3; Figure 4dHow it will be judged
Na+ currents evoked by 25 ms steps from -80 to 0 mV in 5 mV increments, leak subtracted (Methods). The Methods do not name the measure compared; readings, (a) the largest peak inward current over the steps, per patch, and (b) the same divided by the patch area estimated from its capacitance at 1 uF/cm2 (Methods). Two-tailed Wilcoxon rank-sum (Fig. 4d legend). Reproduced when, under both readings, the VEN median is lower with p < 0.05 (conventional); blocked as methods_underspecified when they disagree.
- fig4i-peak-index-ais-distance
The phase peak index decreases linearly with AIS distance from the soma in the VEN model, and this relation closely matches the one in real neurons.
the linear decrease in the phase peak index with increasing AIS distance observed in the VEN model closely matched the experimental data (Fig. 4i , ANCOVA: F(1, 93) = 1.07, P = 0.5729 for intersection, P = 0.0031 for slope)
Results, The AIC evolved a neural signal-processing strategy, paragraph 4; Figure 4iHow it will be judged
Phase peak index as in the Methods (Calculation of the phase peak index), against AIS distance; real neurons binned by AIS distance as in the Fig. 4i legend (n = 62, each point a mean of 2 to 30 neurons; the bins are not given, a standard choice). Reproduced when the slope is negative with two-tailed t-test p < 0.05 in the model and in real neurons, and the ANCOVA term for intercept (model against real neurons) gives p >= 0.05. The paper does not say what its ANCOVA "slope" P (0.0031) tests; readings, (a) the common slope against zero, which fits "closely matched", and (b) the difference of slopes between model and data, under which the printed P would mean the slopes differ. The slope term is reported under both and does not decide the outcome. The printed F(1, 93) = 1.07 gives p near 0.30, not 0.5729, and the 93 degrees of freedom do not follow from the n stated.
- fig4g-model-ais-distance-ap-shape
In the VEN model, moving the AIS farther from the soma makes APs wider and smaller and the phase-plane plot more saddle-like; this effect is not replicated in the PC model.
Crucially, simulating an increase in the distance of the AIS from the soma in the VEN model led to APs being wider and smaller in amplitude, and the phase–plane plot becoming more ‘saddle-like’, (Fig. 4g and Extended Data Fig. 7b ). This effect was not replicated in the PC model (Fig. 4h ).
Results, The AIC evolved a neural signal-processing strategy, paragraph 4; Figure 4g,h; Extended Data Figure 7bHow it will be judged
Simulations as in the Methods (Computational model), AIS distance varied 0 to 170 um along the thick basal dendrite in the VEN model and hillock length 0 to 70 um in the PC model. Reproduced when, in the VEN model, AP amplitude falls and AP width rises with AIS distance, each slope with two-tailed t-test p < 0.05 (Extended Data Fig. 7b legend), and the phase peak index falls. In the PC model the legend reports small but significant changes (amplitude slightly larger, p < 0.0001; width slightly wider, p = 0.0013), so "not replicated" is read as no fall in amplitude and no saddle-like phase-plane plot, not as the absence of any significant change.
- fig4j-eepsp-latency
Latencies of eEPSPs evoked by deep-layer stimulation do not differ between paired VENs and PCs (5.13 and 5.02 ms).
The postsynaptic response latencies were similar between VENs and PCs (5.13 ± 0.29 ms for VENs and 5.02 ± 0.30 ms for PCs, two-tailed paired t -test: P = 0.8941)
Results, VENs respond robustly to deep-layer synaptic input, paragraph 1; Figure 4jHow it will be judged
A claim of absence, judged on the paper's two-tailed paired t-test at alpha 0.05; reproduced when p >= 0.05, with the mean difference reported. Tolerances are the stated s.e.m.
- fig4j-eepsp-amplitude
eEPSP amplitudes are higher in VENs than in adjacent PCs, with effects of cell type and stimulation level in an ANOVA.
whereas the response amplitudes in VENs were significantly higher than those in adjacent PCs (analysis of variance (ANOVA), P = 0.0034 for cell type and P < 0.001 for stimulation level
Results, VENs respond robustly to deep-layer synaptic input, paragraph 1; Figure 4jHow it will be judged
Two-way ANOVA of amplitude on cell type and stimulation level, as in the code's Fig4j_plot_EPSPcmp.m. Reproduced when VEN amplitudes are higher and the cell-type effect has p < 0.05 (conventional).
- model-ven-fires-more
In simulations, the VEN model fires more than the PC model to the same synaptic input trains, and a distal axon origin raises the somatic response to distal basal inputs.
VEN fired more robustly than PC to the same synaptic input trains (Fig. 4k ), and the distal origin of the axon facilitates the somatic response to the distal basal dendritic inputs (Fig. 4l )
Results, VENs respond robustly to deep-layer synaptic input, paragraph 2; Figure 4k,lHow it will be judged
Reproduced when, across the input frequencies of 200 to 1,100 Hz (Methods), the VEN model's firing rate exceeds the PC model's, and the VEN model with AIS D = 70 um fires more than with AIS D = 0 um.
- fig5-connectivity-total
Of 1,292 potential connections among 377 layer 5b neurons, 31 monosynaptic connections were found.
In total, we tested 1,292 potential connections from an additional set of 377 neurons in layer 5b and confirmed 31 monosynaptic connections.
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 2; Figure 5d - fig5-connectivity-by-type
PCs connect to PCs in 24 of 503 pairs, VENs make no connections to VENs (0 of 110) or PCs (0 of 200), PCs connect to VENs in 1 of 200, PCs and INs connect in 2 and 4 of 65, and no VEN-IN connections occur (0 of 55 each way).
PCs formed monosynaptic connections with other PCs in 24 out of 503 tested pairs ... VENs did not form synaptic connections with adjacent VENs (VEN-to-VEN, 0 of 110, 135.7 ± 60.0 μm) or with PCs (VEN-to-PC, 0 of 200, 119.3 ± 63.1 μm) ... (PC-to-VEN, 1 of 200 ... (PC-to-IN, 2 of 65 and IN-to-PC, 4 of 65 ... (VEN-to-IN, 0 of 55 and IN-to-VEN, 0 of 55
Results, Altered connectivity profile of deep-layer AIC neurons, paragraph 2; Figure 5iHow it will be judged
Counts are integers, so 10% of 0, 1 or 2 is no tolerance; those counts must match exactly. Connections are uEPSPs or uIPSPs evoked by single presynaptic spikes, averaged over more than 20 trials (Fig. 5f legend), with uEPSPs measured at -70 mV and uIPSPs at -60 mV (Methods); cell types as identified by firing pattern and post hoc morphology (Methods), taken from the deposit's labels. The paper gives no amplitude or latency criterion for a connection, so the deposit's own connection annotations are used; if it has none, the claim is blocked as methods_underspecified.
- fig6-ven-subtype-morphology
VEN-L has a larger basal dendritic arborization than L5 PCs, VEN-S an intermediate one similar to PCs; the axon origin lies farther from the soma in both VEN subtypes than in PCs, with no difference between VEN-L and VEN-S.
VEN-L had larger basal dendritic arborization than L5 PCs, whereas VEN-S had intermediate-sized basal dendrite arborization similar to PCs ... the distance from the axon originating site to the soma was significantly greater in both VEN subtypes compared with PCs (Fig. 6e ), with no significant difference observed between VEN-L and VEN-S
Results, Multimodal profiling of two VEN subtypes, paragraph 1; Figure 6c-eHow it will be judged
Two-tailed Wilcoxon rank-sum tests with Benjamini-Hochberg FDR (Fig. 6d,e legend), n = 38 VEN-L, 34 VEN-S, 85 PCs for basal height and field size, and 36, 20 and 74 for axon distance. Reproduced when VEN-L basal field exceeds PCs at FDR < 0.05, VEN-S does not differ from PCs, both subtypes exceed PCs in axon distance at FDR < 0.05, and VEN-L against VEN-S gives FDR >= 0.05.
- fig6f-g-ven-subtype-mapping
VEN-Ls map to L5 ET (Exc FEZF2 DSG2, n = 10) and VEN-Ss to L5/6 CT (Exc FEZF2 COL24A1, n = 11), where they fall in the subcluster COL24A1 POC5 apart from canonical L5/6 CT neurons.
the morphologically defined VENs mapped to L5 ET (Exc FEZF2 DSG2) were VEN-Ls ( n = 10), while those VENs mapped to L5/6 CT (Exc FEZF2 COL24A1) were VEN-Ss ( n = 11) ... VEN-Ss were specifically assigned to the subcluster COL24A1 POC5, whereas the canonical L5/6 CT neurons ( n = 10) mapped to the other subclusters
Results, Multimodal profiling of two VEN subtypes, paragraph 2; Figure 6f,g - fig6h-subtype-markers
VEN-L expresses markers such as DSG2, HAPLN4, TOX2, TRPC4, CAMK1G and TAGLN2; VEN-S expresses ATP8A2, POC5 and SEMA3E.
VEN-L expressed markers such as DSG2, HAPLN4, TOX2, TRPC4, CAMK1G and TAGLN2 , whereas VEN-S showed high expression of ATP8A2, POC5 and SEMA3E
Results, Multimodal profiling of two VEN subtypes, paragraph 2; Figure 6hHow it will be judged
Groups as in the Fig. 6h legend, the scRNA-seq cluster Exc FEZF2 DSG2 (VEN-L) and the subclusters of Exc FEZF2 COL24A1 from Fig. 6g (COL24A1 POC5 for VEN-S, the others L5/6 CT). Differential expression with SCANPY's Wilcoxon test (Methods, Enrichment marker genes). The Methods give two levels, (a) significant marker genes, log fold change > 1 and FDR < 0.05, and (b) enriched marker genes, among the top 50 ranked and meeting the four expression criteria listed there; the text does not say which the named genes meet. Reproduced when each named gene passes for its subtype under both; blocked as methods_underspecified when they disagree.
- ven-subtypes-similar-physiology
VEN-L and VEN-S have similar physiological properties.
Despite their distinct morphological and transcriptomic profiles, both VEN subtypes exhibited similar physiological properties (Extended Data Fig. 9 and Supplementary Table 8 )
Results, Multimodal profiling of two VEN subtypes, paragraph 2; Extended Data Figure 9c,d; Supplementary Table 8How it will be judged
A claim of absence, judged on the paper's test, two-tailed Wilcoxon rank-sum with Benjamini-Hochberg FDR (Extended Data Fig. 9c,d), on AP width and amplitude of 85 VEN-L and 41 VEN-S. Reproduced when neither is significant at FDR 0.05. The other features are in Supplementary Table 8, not read.
- fig7c-tau-rna-distance
Across pairs of projection neuron types, distances in membrane time constant correlate with transcriptomic distances (r = 0.53).
Pooling the pairs across all clusters revealed a high correlation ( r = 0.53) between the membrane time constant (tau) distances and RNA distances (Fig. 7a–c )
Results, Transcriptomic distinctions underlie phenotypic variation, paragraph 1; Figure 7a-cHow it will be judged
Per pair of projection neuron types, the transcriptomic distance from the Pearson correlation of mean log2(x + 1) counts over the 500 most-variable genes of the 10x data, and the tau distance as the Euclidean distance between type means (Methods, Variability analysis of transcriptomic neuron types); Pearson r over all pairs (Fig. 7c legend). The Methods call the transcriptomic distance "the Pearson correlation" and the Results "correlation distance"; it is taken as 1 - r, the reading under which a positive r between distances is possible, and the notebook says so.
- fig8a-metabolite-gradient
Of 581 metabolites, 228 differ between AIC and V1 and only 108 between AIC and parietal cortex.
we identified 228 differentially abundant metabolites between the AIC and V1 (Welch's ANOVA test followed by Games–Howell test, P < 0.05) compared with only 108 between the AIC and PrC
Results, Cortical metabolomics reveals a glycolytic bias of the AIC, paragraph 1; Figure 8aHow it will be judged
Welch's ANOVA followed by Games-Howell at P < 0.05 per metabolite (a selection threshold), on 6 AIC, 6 PrC and 7 V1 samples from three animals (Fig. 8 legend).
- fig8de-glycolytic-bias
Compared with V1, AIC shows elevated citrate, reduced 2-ketobutyrate and increased glutamate, with altered expression of oxidative enzyme genes, read as a glycolytic bias.
AIC cells displayed elevated citrate and reduced 2-ketobutyrate levels, along with increased glutamate
Results, Cortical metabolomics reveals a glycolytic bias of the AIC, paragraphs 3 and 4; Figure 8d,eHow it will be judged
Welch's ANOVA followed by Games-Howell test (Fig. 8 legend). Reproduced when citrate and glutamate are higher and 2-ketobutyrate lower in AIC than in V1 at P < 0.05.
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