Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation (DANDI:000005)

Claims

From the paper Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation

Deprecated: Its claims were written from the abstract only. Read against the full text on 2026-10-20, the criteria of exc-mainly-touch and fs-enhance-touch-selectivity test measures the paper does not use, and seven of the paper's findings on this data have no claim. Its outcomes are shown but not counted.

Reproducing Yu et al. (2016) from dandiset 000005 7

Notebook reproduce_yu_2016.ipynb

Not reproducedResults, Dynamics of L4 fast-spiking interneurons, paragraph 3; Figure 5b,d,e
L4 excitatory neurons respond mostly to touch (0.3 +- 0.4 spikes per touch, n = 85) and only weakly to whisker movement; their rate does not change significantly between nonwhisking and whisking (0.4 to 0.6 spikes/s, P = 0.20).
Excitatory neurons responded mostly to touch (mean ± s.d., 0.3 ± 0.4 spikes per touch; median, 0.1 spikes per touch; n = 85 neurons; Fig. 5b,d) and showed weak response to whisker movement ... (nonwhisking ... 0.4 ± 0.6 spikes per s; median, 0.1 spikes per s; whisking ... 0.6 ± 0.9 spikes per s; median, 0.2 spikes per s; n = 85, P = 0.20; Fig. 5d,e). In contrast to VPM and L4 FS neurons, L4 excitatory neurons responded selectively to touch
Results, Dynamics of L4 fast-spiking interneurons, paragraph 3; Figure 5b,d,e
What the paper reports
- nonwhisking against whisking spike rate over L4 excitatory neurons: p = 0.2 (n = 85 neurons)
Touch selectivity of the 18 included excitatory cells (median 0.980) is not significantly higher than that of FS cells (0.916, one-sided Mann-Whitney p = 0.074) or VPM units (0.883, p = 0.090). The test is fragile. Selectivity rests on few spikes (median 23 in the 25 ms after touches; 8 of 18 cells at exactly 0 or 1). Without the mice flagged as lacking touch input the excitatory cells are more selective than both groups (p = 0.024 and 0.038), and so are the 12 excitatory cells with at least 20 spikes in the touch windows (p = 0.003 and 0.005). These do not decide the outcome, as the flag is inferred from touch responses and both selections favour the claim. Only isolated touches gives p = 0.084 and 0.131; widths of 0.7 ms gives 0.112 and 0.126. The measures the criterion reports go the claim's way, 0.28 of excitatory cells are modulated by whisking against 0.80 of FS cells (Fisher p = 0.0016) and 0.88 of VPM units (p = 0.00011), and a selectivity built from the whisking-minus-rest rate is higher than both (p = 0.047 and 0.032). 0.56 of excitatory cells are touch-responsive (FS 0.65, VPM 0.83). Of the 53 untagged whole-cell cells, 26 have fewer than 5 spikes and 5 more too few spikes or touches, so the group holds the cells that fire most, against the 37 whole-cell excitatory cells of the paper.
How the test differed from the paper’s method
- Excitatory cells are identified here as untagged whole-cell cells with action potentials at least 0.6 ms wide at half maximum (22 cells). The paper's excitatory group also holds cell-attached cells (Supplementary Table 2) and leaves out ION-transected mice, which the files do not mark.
- The touch selectivity index is a choice made here; the paper's measure is not known.
Not reproducedResults, Layer 4 FS interneurons suppress reafference in L4, paragraph 1; Figure 8d
With PV interneurons suppressed, L4 excitatory neurons become driven by whisker movement (whisking rate above nonwhisking, P = 0.02), while in control trials they are not (P = 0.55); their selectivity for touch is normally maintained in part by FS interneurons.
L4 excitatory neurons were instead driven by whisker movements (P = 0.02, Fig. 8d), implying that their selectivity for touch was normally maintained in part by FS interneurons.
Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 1; Figure 8d
What the paper reports
- nonwhisking against whisking rate in eNpHR trials (Fig. 8d): p = 0.02 (n = 40 neurons)
- nonwhisking against whisking rate in control trials (Fig. 8d, printed in the figure): p = 0.55 (n = 40 neurons)
Touch selectivity inside the light window is lower with light in 2 of 6 excitatory cells (median 0.083 without light, 0.949 with; one-sided Wilcoxon p = 0.953). The touch response rises with the light (median 0.4 to 8.62 Hz, 5 of 7) more than the whisking modulation does. Without light three cells sit at selectivity 0 because their touch response in the window is below zero, on 0 to 13 spikes after touches, so the measure is near its floor there. In the 30 juxtacellular PV-Cre cells not suppressed by light, selectivity is lower with light in 14 (median 0.885 against 0.881, p = 0.613). The first (uncorrected) version gives lower selectivity in 1 of 5.
How the test differed from the paper’s method
- As for fs-suppress-movement-spiking; the selectivity index is a choice made here, and the touch counts inside the light window are smaller than over whole trials.
ReproducedResults, Chronic extracellular recordings from somatosensory thalamus, paragraph 1; Figure 1b,d; Figure 5b,c
VPM neurons respond to active touch with a sharp, short-latency increase in spike rate (0.6 +- 0.5 spikes per touch, median 0.4; latency 3.2 +- 1.0 ms, median 2.5 ms).
Neurons responded to active touch during behavior with an increase in spike rate (Fig. 1b). The peristimulus time ... histogram aligned to touch onset showed a sharp peak in spike rate (mean ± s.d., 0.6 ± 0.5 spikes per touch; median, 0.4 spikes per touch), with short latency after touch onset (mean ± s.d., 3.2 ± 1.0 ms; median, 2.5 ms)
Results, Chronic extracellular recordings from somatosensory thalamus, paragraph 1; Figure 1b,d; Figure 5b,c
20 of 24 included VPM units (0.83) fire more 0 to 25 ms after a touch onset than 25 to 0 ms before it (one-sided Wilcoxon over touches, p < 0.01); 0 of 24 with spikes moved to the next trial. Median touch response 7.5 Hz (rate 25.0 Hz after, 14.4 Hz before). At least one responsive unit in each of the 6 mice. 5 of 29 units were dropped for too few spikes or touches in trials without light.
How the test differed from the paper’s method
- The full text was not available; the touch window, the test and the threshold are choices made here, and no number of the paper is compared.
ReproducedResults, Chronic extracellular recordings from somatosensory thalamus, paragraphs 1 and 2; Figure 1c,e; Figure 5d,e; Supplementary Figure 2b,c
VPM neurons fire at 5.1 +- 5.5 spikes/s without whisker movement or touch; most (25 of 29) increase their rate during whisking without touch, and the mean rate rises from 5.1 to 13.5 spikes/s. Three of 29 do not increase with whisking but still respond to touch.
Typical VPM neurons showed significant spike rates (mean ± s.d., 5.1 ± 5.5 spikes per s; median, 3.3 spikes per s; n = 29 neurons), even in the absence of whisker movement and touch. ... Most VPM neurons increased their spike rate during whisking in the absence of touch (25 out of 29 neurons ... The average spike rate increased severalfold after onset of whisker movement (from 5.1 ± 5.5 spikes per s to 13.5 ± 12.7 spikes per s; P = 4 × 10−6; n = 29 neurons, Wilcoxon signed-rank test
Results, Chronic extracellular recordings from somatosensory thalamus, paragraphs 1 and 2; Figure 1c,e; Figure 5d,e; Supplementary Figure 2b,c
What the paper reports
- nonwhisking against whisking spike rate over VPM neurons: Wilcoxon signed-rank test, p = 4 × 10⁻⁶ (n = 29 neurons)
21 of 24 VPM units (0.88) are modulated by whisking phase away from touch under the occupancy-corrected test with a trial-shift null (p < 0.01), against 0.12 with spikes moved to the next trial, so the test marks about ten times its nominal rate on the null; this does not bring 0.88 near 0.5. 23 of 24 fire more during whisking than at rest (median 12.78 against 3.78 Hz, p = 1.2e-06). With a 5 degree whisking threshold, 0.92. One mouse (2 units) has no modulated unit. The paper's measure (r2 of a sinusoid fit above 0.25) marks 0.96, but it marks 0.33 to 0.40 of L4 cells with spikes moved to the next trial. The first version of the test (Rayleigh) gave 0.92 with the true alignment and 0.88 with the wrong one.
How the test differed from the paper’s method
- The whisking test of the claims file (a Rayleigh test of spike phases) was replaced after the first run, because its null control marked 0.88 of units as modulated with spikes in the wrong trial; the claims file records the amendment and what had been seen. Both versions are shown.
- The whisking band (6 to 30 Hz), threshold (2.5 degrees) and the measure are choices made here. The paper judges modulation by the r2 of a sinusoid fit (Supp. Fig. 2e), read after the criteria were written; it is shown as a variant.
ReproducedResults, Dynamics of L4 fast-spiking interneurons, paragraph 3; Figure 5b,d; Supplementary Figure 7
Touch- and whisking-evoked spikes are typically multiplexed in individual L4 FS neurons, as in VPM neurons.
Touch- and whisking-evoked spikes were typically multiplexed in individual L4 FS neurons (Fig. 5b,d and Supplementary Fig. 7), as in VPM neurons.
Results, Dynamics of L4 fast-spiking interneurons, paragraph 3; Figure 5b,d; Supplementary Figure 7
20 tagged cells (10 mice) are included; 13 (0.65) are touch-responsive, 16 (0.80) are modulated by whisking phase, 11 are both. Median touch response 34.9 Hz, whisking modulation 2.64 Hz (VPM 1.30 Hz, Mann-Whitney p = 0.085). Unchanged with tag thresholds 0.1 and 0.3. 4 of the 20 come from 2 mice flagged as lacking touch input (probably ION-transected) and none of them responds to touch; without them 0.81 of 16 are touch-responsive and 0.81 modulated. With the paper's r2 measure, 0.80 are modulated. With spikes moved to the next trial, 0 of 20 pass either test. 3 of 23 tagged cells were dropped for lack of a named principal whisker; 2 included cells have fewer than 99 null draws, so p < 0.01 was out of reach for them.
How the test differed from the paper’s method
- FS cells are identified here as cells spiking within 6 ms of isolated 5 ms light pulses in VGAT-ChR2 mice (23 cells, all tagged from the vS1 site or the site labelled VPM and vS1, at 1.6 to 4.6 ms latency). The paper also requires a spike waveform inside a boundary of peak-to-trough ratio and duration (Supp. Fig. 6), not given in numbers, so the tagged cells may include non-FS interneurons.
- The files do not mark ION-transected mice, so their cells are in the group; leaving out the mice flagged as lacking touch input is shown as a variant.
- The whisking test was amended as for vpm-whisking.
ReproducedResults, Layer 4 FS interneurons suppress reafference in L4, paragraph 1; Figure 8b-d; Supplementary Figure 13b
Partially suppressing PV (FS) interneurons increases the spike rate of L4 excitatory neurons during nonwhisking (0.6 to 1.6 spikes/s) and whisking (0.8 to 2.7 spikes/s).
Partially suppressing PV (FS) interneurons changed the responses of excitatory neurons (Fig. 8b–e; P = 1 × 10−6, Kruskal-Wallis test). L4 excitatory neurons increased their spike rate during both nonwhisking periods (from 0.6 ± 0.1 spikes per s to 1.6 ± 0.3 spikes per s; mean ± s.e.m., n = 40 neurons, P = 6 × 10−5) and whisking periods(from 0.8 ± 0.2 spikes per s to 2.7 ± 0.5 spikes per s, P = 2 × 10−6
Results, Layer 4 FS interneurons suppress reafference in L4, paragraph 1; Figure 8b-d; Supplementary Figure 13b
What the paper reports
- rates of excitatory neurons across conditions: Kruskal-Wallis test, p = 10⁻⁶ (n = 40 neurons)
- nonwhisking rate, control against eNpHR: p = 6 × 10⁻⁵ (n = 40 neurons)
- whisking rate, control against eNpHR: p = 2 × 10⁻⁶ (n = 40 neurons)
In PV-Cre mice, inside the vS1 light window (about 0.8 to 2.3 s after the trial start), the rate of excitatory cells during non-touch whisking rises in 6 of 7 cells (median 0.05 Hz without light, 1.07 Hz with; one-sided Wilcoxon p = 0.016), from 4 mice; the seventh has no spikes during whisking in either condition. The evidence is thin. 4 cells come from anm266945 (without it 3 of 3 rise, p = 0.125), and several rates rest on 0 to 10 spikes. Over the whole light window 5 of 7 rise (p = 0.188), and the phase modulation rises in 3 of 6 (p = 0.219). The mice whisk and touch about as much with light as without (0.35 against 0.29 s of whisking, 3.4 against 3.6 touches per trial). The PV-Cre juxtacellular cells not suppressed by light, mostly excitatory by Supplementary Table 2 (38 of 42 cell-attached PV-Cre cells), rise in 24 of 32 (p = 0.00042), but that selection is biased toward a rise and does not decide the outcome. The light cuts the firing of 3 PV-Cre cells by more than half, as for the 3 of 4 PV cells inhibited in Supp. Fig. 13a.
How the test differed from the paper’s method
- The supplement (read after the first run) states that this light drives eNpHR in PV cells; the files do not name the opsin.
- 7 whole-cell excitatory cells decide; the paper's PV-Cre excitatory cells are mostly cell-attached, and the juxtacellular cells are shown as a variant.
ReproducedResults, Inhibition is driven by thalamus, paragraph 2; Figure 6d,e; Supplementary Figure 9j
Photoinhibiting the thalamus reduces the spike rates of L4 FS interneurons during nonwhisking (to 4% of control), whisking (to 13%) and touch (to 32%), so FS interneurons are driven by thalamic input.
Photoinhibition reduced spike rates in FS interneurons during nonwhisking (to 4% of control ... and whisking epochs (to 13% of control ... as well as in response to touch (to 32% of control ... FS interneurons were thus driven by input from the thalamus.
Results, Inhibition is driven by thalamus, paragraph 2; Figure 6d,e; Supplementary Figure 9j
What the paper reports
- nonwhisking spike rate with and without thalamic photoinhibition: p = 5 × 10⁻⁴ (n = 13 neurons)
- whisking spike rate with and without thalamic photoinhibition: p = 6 × 10⁻⁵ (n = 15 neurons)
- touch response with and without thalamic photoinhibition: p = 10⁻⁴ (n = 14 neurons)
With light at the site labelled VPM (250 pulses over 0.32 to 2.82 s, 100 Hz as in Supp. Fig. 9i), the rate of all 9 tagged FS cells falls (median 17.9 to 7.7 Hz, median ratio 0.40, one-sided Wilcoxon p = 0.00195), and so does their rate during non-touch whisking (9 of 9). The mice whisk less with the light (0.60 against 0.99 s per trial in the window, touches 5.13 against 4.45), so the whisking-period rate is the stronger evidence. The cells come from 2 mice. The drop is not specific to FS cells; 18 of 21 cells recorded with this light fire less.
How the test differed from the paper’s method
- The VPM-site light in VGAT-ChR2 mice is taken as the paper's thalamic photoinhibition, which the supplement describes as a 100 Hz train of 5 ms pulses; the files do not say what the light does, and its wavelength is given as 594 nm.

Not tested in a notebook 1

1 metadata insufficient

BlockedResults, Inhibition is driven by sensory input, paragraph 3; Figure 7h,i· Metadata insufficient
After ION transection, the whisking-related activation of L4 FS interneurons is absent in most cells (P = 0.80, n = 10), so their movement-related modulation is reafference driven by sensory input.
In addition, whisking-related activation of FS interneurons was also absent in most cells (P = 0.80, n = 10 neurons; Fig. 7h,i). ... These data show that excitation of L4 excitatory neurons and L4 FS neurons is dominated by sensory input. Modulation correlated with whisker movement in L4 FS neurons constitutes reafference.
Results, Inhibition is driven by sensory input, paragraph 3; Figure 7h,i
What the paper reports
- nonwhisking against whisking spike rate of FS cells after ION cut: p = 0.8 (n = 10 neurons)
The supplement (Supp. Figs. 6, 11 and 12) shows the test, the spike-phase relationship of FS cells in control and ION-transected mice. Supplementary Table 2 counts 9 transected VGAT-ChR2 mice with 9 whole-cell excitatory and 10 cell-attached FS cells. The files hold as many VGAT-ChR2 cells per recording mode as the table, but no file marks the transected mice; the files hold no surgery, notes or lesion field. The notebook flags 4 mice whose cells have no touch input (anm273341, anm275231, anm318530, anm318532), with a rule chosen after seeing the values. Their 4 included tagged cells respond to touch in none, are modulated by whisking in 3, with lower modulation (1.12 against 2.90 Hz in 16 cells of 8 other mice, p = 0.061) and no lower sinusoid r2 (0.50 against 0.53). This is not a test of the claim. The light at the site labelled vM1 is not part of the paper's described test.

Findings about the data

What attempts found about the dataset itself, for its owner and the archive.

Description missingNo L4 file names the cell type of its neuron (excitatory or FS). The cell types the paper compares can only be inferred from the data, here from light tagging in VGAT-ChR2 mice and from action potential width.
Description missingNo file marks the mice whose infraorbital nerve was transected (9 VGAT-ChR2 mice in Supplementary Table 2 of the paper), and the files hold no surgery or notes field. Their cells cannot be told from control cells except by inference; 4 mice whose cells have no touch input are probably among them. This blocks the test of Figure 7, and these cells may be mixed into any analysis of control cells.
Metadata errorThe genotype is missing for the 6 VPM mice (VGAT-ChR2-EYFP in Supplementary Table 1) and for 3 L4 mice (anm260074 VGAT-ChR2-EYFP, anm223517 PV-IRES-Cre x Ai32, anm250509 PV-ChR2), and the 5 SOM-IRES-Cre x Ai32 mice are given as Ai32.
Description missingEvery L4 file gives cortical layer 4 (depth 0.42 to 0.62 mm), though the paper's waveform analysis (Supp. Fig. 6) includes L5 cells; the layer of each cell cannot be checked.
Description missingThe optogenetic conditions are not described. `photo_stim_mode` has an empty description and its labels do not map to one kind of light (VPM-site pulse trains are labelled `5ms_pulse` in early files and `shift` in later ones); `photo_stim_power` is NaN in every L4 file; no file names the opsin. The light epochs can be read only from the photostimulation series.
Metadata errorThe session description gives the wrong recording mode for 24 of 130 L4 files, all from PV-Cre mice. 23 described as whole-cell hold traces near 0 mV with small extracellular spikes, as juxtacellular recordings do, and one described as juxtacellular sits near -65 mV. By the trace, PV-Cre has 9 whole-cell and 39 juxtacellular cells where Supplementary Table 2 has 5 and 42.
Metadata errorIn the L4 files the trial table's `first_touch_time` is the trial start plus the true first-touch latency divided by 1000 (it matches the touch onset series within 2 ms in 0.956 of trials once multiplied by 1000). In the VPM files it is correct.
Description missingThe L4 trace is sampled at 10 kHz in files up to March 2015 and at 20 kHz from late August 2015 on, with trials of 5.2 or 5.5 s at 10 kHz and 5.9 s at 20 kHz; nothing but the timestamps states the rate.
Description missing8 files name no principal whisker, and the VPM files give one principal whisker per file though the session description says each unit has its own.
OtherThe light at the site labelled VPM in VGAT-ChR2 mice is given as 594 nm, and isolated pulses at the site labelled vS1 (594 nm) evoke short-latency spikes in VGAT-ChR2 cells; these wavelengths may be worth checking against the experiment.
Methods not availableThe paper's full text is not open access and neither it nor the dandiset links analysis code. The public supplement names the measures (a sinusoid fit of rate against phase, a waveform boundary for FS cells) but not their windows, bins or boundaries.

Notebooks

Every registered entry that uses this dataset. An entry can hold several notebooks, and can use more than one dataset.

Reproduction VPM and layer 4 responses to touch and whisking (Yu et al. 2016)

Tests the findings stated in the abstract of Yu, Gutnisky, Hires and Svoboda (2016) on dandiset 000005, which holds silicon probe recordings in VPM and single-cell recordings in layer 4 of barrel cortex of mice locating a pole with their whiskers. It measures touch responses and whisking modulation of VPM units, light-tagged GABAergic (FS) cells and broad-spiking excitatory cells, and the effect of the PV-Cre and VPM-site light. The full text is not open access. All files

Reproducing Yu et al. (2016) from dandiset 000005
reproduce_yu_2016.ipynbExecuted, with outputs · Source

Verification

Round 1
2026-10-19Agreed with 8 of 8 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The handover of the first run, the executed notebook with the conclusions and summary removed, the helper module and the claims file. The verifier also read the paper's public page, with the supplementary legends.
Round 2
2026-10-19Agreed with 8 of 8 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The full executed notebook of the revised run, with its conclusions and summary, the helper module, the claims file, the README and this record. The verifier also downloaded the supplement and checked the figures quoted from it.

Method differences

How the tests differed from the paper’s method or data, and the claims each applies to.

The full text was not available; the touch window, the test and the threshold are choices made here, and no number of the paper is compared.vpm-touch
The whisking test of the claims file (a Rayleigh test of spike phases) was replaced after the first run, because its null control marked 0.88 of units as modulated with spikes in the wrong trial; the claims file records the amendment and what had been seen. Both versions are shown.vpm-whisking
The whisking band (6 to 30 Hz), threshold (2.5 degrees) and the measure are choices made here. The paper judges modulation by the r2 of a sinusoid fit (Supp. Fig. 2e), read after the criteria were written; it is shown as a variant.vpm-whisking
FS cells are identified here as cells spiking within 6 ms of isolated 5 ms light pulses in VGAT-ChR2 mice (23 cells, all tagged from the vS1 site or the site labelled VPM and vS1, at 1.6 to 4.6 ms latency). The paper also requires a spike waveform inside a boundary of peak-to-trough ratio and duration (Supp. Fig. 6), not given in numbers, so the tagged cells may include non-FS interneurons.fs-touch-and-whisking
The files do not mark ION-transected mice, so their cells are in the group; leaving out the mice flagged as lacking touch input is shown as a variant.fs-touch-and-whisking
The whisking test was amended as for vpm-whisking.fs-touch-and-whisking
Excitatory cells are identified here as untagged whole-cell cells with action potentials at least 0.6 ms wide at half maximum (22 cells). The paper's excitatory group also holds cell-attached cells (Supplementary Table 2) and leaves out ION-transected mice, which the files do not mark.exc-mainly-touch
The touch selectivity index is a choice made here; the paper's measure is not known.exc-mainly-touch
The supplement (read after the first run) states that this light drives eNpHR in PV cells; the files do not name the opsin.fs-suppress-movement-spiking
7 whole-cell excitatory cells decide; the paper's PV-Cre excitatory cells are mostly cell-attached, and the juxtacellular cells are shown as a variant.fs-suppress-movement-spiking
As for fs-suppress-movement-spiking; the selectivity index is a choice made here, and the touch counts inside the light window are smaller than over whole trials.fs-enhance-touch-selectivity
The VPM-site light in VGAT-ChR2 mice is taken as the paper's thalamic photoinhibition, which the supplement describes as a 100 Hz train of 5 ms pulses; the files do not say what the light does, and its wavelength is given as 594 nm.thalamus-drives-fs

Provenance

Attempt record: 000005-yu-2016-01
Paper: Layer 4 fast-spiking interneurons filter thalamocortical signals during active somatosensation
Date: 2026-10-19
Made by: An agent, run by CatalystNeuro
Dataset: DANDI:000005
Version: 0.220126.1853 (doi:10.48324/dandi.000005/0.220126.1853)
Run on: GitHub Actions
Harness: Claude Code (GitHub Actions)
Model: claude-opus-5-5
Protocol: pilot-7

Transcripts of the agent runs

Each run’s prompt, messages and tool calls, with long output cut and the text of the paper left out, and its final report.

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