Dandiset 001538 · Reproduction registry

Claims

From the paper State-dependent modulation of spiny projection neurons controls levodopa-induced dyskinesia in a mouse model of Parkinson’s disease

Reproducing Zhai et al. (2025) from dandiset 001538 30

Notebook reproduce_zhai_2025.ipynb

Not reproducedFigure 5F; the paper's tables at Zenodo doi:10.5281/zenodo.17307059uses data from outside the dandiset
The dandiset's GRAB-ACh recordings are regions of the paper's Figure 5F, and the normalised areas computed from them agree with the paper's per-region values.
The dandiset holds one region per mouse, 11 of the paper's 34 (3 of 13 unlesioned, 3 of 10 6-OHDA, 5 of 11 off-state). The paper's regions have no identifier linking them to mice; by the nearest vector of single-pulse areas only 5 of 11 mice have a paper region within 0.05 on every treatment (the 20240402 mouse within 0.007), so the regions cannot be identified. One paper region is the best match of two off-state mice; with each region used once, 5 of 11 are still within 0.05.
How the test differed from the paper’s method
- The stimulus time is taken from the trial table (3 s after the trial start in six files), where the paper's script fixes 10 s.
Not reproducedFigures 8B, 8C and 10B; the paper's tables at Zenodo doi:10.5281/zenodo.17307059names its codes from outside the dandiset
The dandiset's AIM score tables are mice of the paper's Figures 8 and 10, with genotypes and scores that agree with the paper's tables.
7 of 9 dandiset mice are in the paper's tables (4124 and 5871 are not). The two Figure 10 mice (5844 control, 5846 M1R deletion) have totals equal to the paper's in all 10 sessions; the five Figure 8 mice (1945, 2519, 2828 and 6572 KO, 2587 wild type) agree in 5 of 25 sessions (for 1945, session 1, 33.5 against 27.0). The dandiset's own genotype labels for the CDGI mice contradict each other, so the paper's labels were used. The paper's tables give session totals only; for the Figure 8 mice they equal neither the dandiset's sums over 20 to 80 min nor, outside those 5 sessions, the sums over all time points (1945 session 1 has four time points summing to 33.5), so the scores differ, not only the time points summed.
How the test differed from the paper’s method
- The paper's session total is taken to be the sum over the session's time points; the Figure 8 mice have 4 time points in some dandiset sessions and 6 in others.
Not reproducedFigure 1I; Results, first section (P = 0.0133, Mann-Whitney)verifier disagreed at first
SCH 23390 reverses the higher dendritic excitability of on-state dSPNs.
The criterion (P < 0.05 with the SCH median lower) is not met, though the difference has the stated direction. On-state with SCH 0.419 (9 cells) against on-state 0.476 (10 cells), P = 0.0662 (exact 0.0653), effect r = -0.51; with the stricter basal-ratio rule P = 0.524. The difference from the paper comes from one cell, SCH 20190411 cell 1, whose index is 0.584 here and 0.228 in the paper's table; the dandiset holds only its second pair of sites. Without that cell P = 0.0266; with the paper's value for it P = 0.016 (exact 0.0133, the paper's P). The other eight SCH cells differ from the paper's values by 2.4% to 10.9%. That the missing sites explain the difference is an inference from the recovered P, as the paper does not list each cell's sites.
How the test differed from the paper’s method
- Matching the SCH cells to the paper's rows by order is an assumption (link-dendritic-cells).
Not reproducedFigure 3F; Results, second section (P = 0.0545)
Sulpiride does not significantly alter dendritic excitability in on-state iSPNs.
The paper's test finds the difference the claim says is absent. On-state with sulpiride 0.506 (7 cells) against on-state 0.339 (10 cells), P = 0.0097, effect r = 0.74; the paper reports P = 0.0545 with 8 and 10 cells, and its own medians go the same way (0.499 and 0.345). With the sites as labelled P = 0.0164, with the stricter basal-ratio rule P = 0.0663. The sulpiride cell without an index (20190508 cell 3, only a distal site in the dandiset) has 0.217 in the paper's table; with that value P = 0.0545, the paper's P. Under the main basal-ratio rule the outcome turns on that one cell; under the stricter rule P = 0.0663 without it, which would also meet the criterion, so the outcome depends on the basal-ratio rule as well. That the missing site explains the difference is an inference from the recovered P, as the paper does not list each cell's sites.
How the test differed from the paper’s method
- One sulpiride cell has no index here (only a distal site).
Partially reproducedFigures 1E, 3C, 6C, 7C and 9D; the paper's tables at Zenodo doi:10.5281/zenodo.17307059uses data from outside the dandiset
The dandiset's somatic current-step recordings are those behind the paper's somatic excitability figures, and the spike counts computed from them agree with the paper's per-cell tables.
Groups are matched by name and every group the dandiset holds has the paper's n (12 of 12 groups, 123 cells). 90 of 123 cells (73.2%) match a row of the paper's table exactly over 20 to 300 pA and 105 (85.4%) within 3 spikes, below the 80% and 95% of the criterion; 108 have the same rheobase as their best match. dSPN on has the fewest exact matches (6 of 15). The best matches are not one-to-one (9 paper rows are the best match of two or three cells); with each row used once, 89 cells (72.4%) match exactly and 103 (83.7%) within 3 spikes. The best-match rows follow the dandiset's order by date and cell number, every cell at its own rank in 8 of 12 groups and 10 of 15, 11 of 15, 11 of 12 and 10 of 11 cells in the others. Of the 14 cells with a repeated step, keeping the last sweep in place of the first gives the same best-match difference in 13 and a closer one in 1.
How the test differed from the paper’s method
- The paper's spike counts come from its script run on Prairie View exports; the differences of 1 to 24 spikes may come from the export or from cells whose steps are missing or repeated in the files (18 cells miss a step, 14 repeat one).
Partially reproducedFigures 2G to 2I and 4F to 4H; the paper's tables at Zenodo doi:10.5281/zenodo.17307059uses data from outside the dandiset
The dandiset's Sr2+-oEPSC recordings are cells of the paper's Figures 2 and 4, and their events agree with the paper's per-cell values.
All 14 dandiset cells match a paper identifier (date and session letter); the paper has 33 cells (17 off, 16 on), so the dandiset holds one cell per mouse. In every cell the detector here finds fewer events (2 to 85, against 29 to 127 in the paper's tables) and a higher mean amplitude than the paper's events; 2 of 14 cells are within 25% on both, and also 2 of 14 when the paper's amplitude is read as its per-cell value (0.70 to 0.96 times the mean of its histogram events). In 20230405b (2 events against 73) the detection window opens on the slow decay of a large synchronous current, and the small events on it stay below the threshold (figure in the notebook). The paper's frequency equals its event count over 3.6 s. With the paper's per-cell amplitudes, on-state dSPNs are all above off-state ones and on-state iSPNs all below (Mann-Whitney P = 0.057 each).
How the test differed from the paper’s method
- Events are found with a threshold detector written here (low-pass 1 kHz, five robust SD, local baseline); the paper used TaroTools with visual verification, which cannot be repeated.
ReproducedFigures 1I, 3F, 6D and 7F; the paper's tables at Zenodo doi:10.5281/zenodo.17307059uses data from outside the dandiset
The dandiset's dendritic line scans are those behind the paper's dendritic excitability index figures, and the index computed from them agrees with the paper's per-cell values.
Three site series hold six trials, two sites under one name; split, they give their cells 0.293, 0.146 and 0.327 against the paper's 0.299, 0.146 and 0.309. With the split, 91 of 92 cells have an index (iSPN on+sul 20190508 cell 3 has only a distal site). Counts of cells with an index equal the paper's n in 9 of 10 groups, and counts of cells with dendritic sites in 10 of 10, so every group is matched, by order or (Figure 6D) by date and letter. Over 91 matched cells the index differs from the paper's by a median of 2.9% (78 within 10%, Spearman 0.938). Two cells differ by more than the paper's value, dSPN on+SCH 20190411 cell 1 (0.584 against 0.228; only its second pair of sites is in the dandiset) and iSPN off 20160524 cell 2 (1.062 against 0.527; its first proximal site has one trial, and without it the cell gives 0.553). The best-match rows of the somatic link follow the dandiset's order (link-somatic-cells), which supports matching by order. With the sites as labelled, 89 of 92 cells have an index.
How the test differed from the paper’s method
- Outside Figure 6D the paper's table has no cell identifiers, so cells are matched by order, an assumption supported by the somatic link.
- The background constants of the paper's script (55 red, 161 green) are used for every session, as the files carry no per-session background.
- Three six-trial series are split into their first and last three trials, the half with the smaller area taken as distal, a choice made here from the data; the sites as labelled are a variant.
ReproducedFigure 1F; Results, first section (P < 0.0001, Mann-Whitney)
In dSPNs the rheobase is lower in the LID on-state than in the off-state.
Rheobase on-state 140 pA against off-state 220 pA (15 cells each from 10 and 8 mice), Mann-Whitney P = 8.86e-06, effect r = -0.95. With one value per mouse P = 0.000425 and complete separation.
ReproducedFigure 1E; Results, first section
In on-state dSPNs suprathreshold current steps evoke more spikes than in off-state dSPNs across a range of intensities.
Summed spikes 20 to 300 pA, median 88 on against 36 off, P = 8.8e-05 (0.00015 for the 22 cells with every step). The on-state median is higher at every step from 120 to 300 pA (per-step P at most 0.012).
How the test differed from the paper’s method
- The paper shows F-I curves without a test; the summed count and its test were chosen here.
ReproducedFigure 1F; Results, first section (P = 0.589, Mann-Whitney)
Bath application of the D1R antagonist SCH 23390 does not reverse the lower rheobase of on-state dSPNs.
Rheobase on-state 140 pA (15 cells) against on-state with SCH 140 pA (10 cells), P = 1.0, effect r = 0.007. In the 5 cells recorded in both conditions the median paired difference is 0 pA (Wilcoxon P = 1.0). Five cells are in both groups, so the unpaired test's samples are not independent; the criterion follows the paper's test.
ReproducedFigure 1I; Results, first section (P = 0.0115, Mann-Whitney)
The dendritic excitability index of dSPNs is higher in the on-state than in the off-state.
Index on-state 0.476 against off-state 0.330 (10 cells each), P = 0.0058 (exact 0.0039), effect r = 0.74; without background P = 0.0046; with a basal-ratio rule of 0.8 to 1.25 (8 cells each) P = 0.0070; with the sites as labelled P = 0.0091.
How the test differed from the paper’s method
- Background constants from the paper's script; basal-ratio rule (0.5 to 2) chosen here, dropping no pair; one six-trial series split into two sites.
ReproducedFigure 3D; Results, second section (P = 0.0013, Mann-Whitney)
In iSPNs the rheobase is higher in the on-state than in the off-state.
Rheobase on-state 160 pA (11 cells, 8 mice) against off-state 120 pA (12 cells, 5 mice), P = 0.000829, effect r = 0.81; one value per mouse P = 0.00899.
ReproducedFigure 3C
The F-I relationship of iSPNs shifts to the right in the on-state.
Summed spikes 65 on against 118.5 off, P = 7.2e-05 (0.000165 for complete cells); lower on-state median at every step from 120 to 300 pA (per-step P at most 0.012).
How the test differed from the paper’s method
- The summed count and its test were chosen here.
ReproducedFigure 3D; Results, second section (rheobase P = 0.287)
Sulpiride does not alter the somatic excitability of on-state iSPNs.
Rheobase on-state 160 pA (11) against on-state with sulpiride 120 pA (7), P = 0.143, effect r = -0.43. The two cells recorded in both conditions have a lower rheobase with sulpiride (160 to 120 and 160 to 100 pA), so the absence rests on the test's power. Those two cells are in both groups, so the unpaired samples are not independent; the criterion follows the paper's test.
ReproducedFigure 3F; Results, second section (P = 0.0029)
The dendritic excitability index of iSPNs falls in the on-state compared with the off-state.
Index on-state 0.339 (10) against off-state 0.524 (10), P = 0.0073 (exact 0.0052), effect r = -0.72; without background P = 0.0073; with the sites as labelled (9 on-state cells) P = 0.0128; dropping sites with fewer than 3 trials P = 0.0091. With the stricter basal-ratio rule (0.8 to 1.25, 9 cells each) P = 0.0774, so the result depends on keeping pairs whose basal ratios differ by more than 25%. The stricter rule moves fig3f-ispn-dendritic-sul-no-change the other way (P = 0.0663, which would meet that criterion).
How the test differed from the paper’s method
- One on-state cell gets its index only from splitting a six-trial series into two sites.
- The Methods keep pairs with similar G0/R0 without a threshold; the 0.5 to 2 rule chosen here drops no pair.
ReproducedFigure 5F; Results, third section (P < 0.0001)
Evoked ACh release (GRAB-ACh3.0) in slices from LID off-state mice is greater than in unlesioned striatum.
Single-pulse normalised area without drug, off-state 0.359 (5 mice) against unlesioned 0.112 (3 mice), P = 0.0357, the smallest attainable (complete separation). Burst stimulation gives the same; the unnormalised dF/F0 area does not (P = 0.25).
How the test differed from the paper’s method
- One region per mouse, 8 of the paper's 24 regions in these two groups.
- Stimulus time from the trial table.
ReproducedFigure 5F; Results, third section (P = 0.4679)
Evoked ACh release in the off-state is similar to that after a 6-OHDA lesion.
6-OHDA 0.240 (3 mice) against off-state 0.359 (5 mice), P = 0.143, effect r = 0.73; burst P = 1.0. With 3 and 5 mice the test detects only complete separation, so the absence is weakly supported.
How the test differed from the paper’s method
- One region per mouse, 8 of the paper's 21 regions in these two groups.
- The test cannot find any difference short of complete separation, so this claim of absence passes with little power.
ReproducedFigure 6C; Results, fourth section
M1R antagonism throughout the off-state does not have a strong impact on the elevated somatic excitability of off-state iSPNs.
Rheobase vehicle 120 pA (8) against antagonist 140 pA (10), P = 0.681, effect r = 0.125; summed spikes P = 0.45.
How the test differed from the paper’s method
- The paper gives no test; its default Mann-Whitney test on rheobase was used.
ReproducedFigure 6D (P = 0.012)
M1R antagonism prevents the off-state elevation of iSPN dendritic excitability.
Index vehicle 0.451 (9) against antagonist 0.269 (7), P = 0.0229, effect r = -0.68; with the stricter basal-ratio rule P = 0.0164.
ReproducedFigures 7A to 7C; Results, fourth section
Deletion of CDGI does not blunt the oscillation of iSPN somatic excitability between on- and off-states.
KO rheobase on-state 210 pA (8) against off-state 140 pA (13), P = 0.00104, effect r = 0.87; summed spikes P = 0.00335.
How the test differed from the paper’s method
- The paper shows F-I curves without a test; a Mann-Whitney test of rheobase was chosen here.
ReproducedFigure 7F (KO P = 0.395; wild type P = 0.0029)
The off-state elevation of iSPN dendritic excitability is absent in CDGI KO mice (off against on not different), while it is present in wild type.
KO index off-state 0.312 (11) against on-state 0.286 (8), P = 0.310, effect r = -0.30 (P = 0.659 with the stricter rule, 0.315 with the sites as labelled); wild type P = 0.0073.
How the test differed from the paper’s method
- One KO off-state cell gets its index only from splitting a six-trial series into two sites.
ReproducedFigures 9C and 9D; Results, fifth section
Deletion of M1Rs from iSPNs does not alter the elevated somatic excitability of off-state iSPNs.
Rheobase control 160 pA (6) against M1R CRISPR 120 pA (8), P = 0.147, effect r = -0.48; summed spikes P = 0.245. The control group is 6 cells from 2 mice, so the absence rests on little power.
How the test differed from the paper’s method
- The paper gives no test; its default Mann-Whitney test on rheobase was used.
ReproducedFigure 1F; Results, first section (both P < 0.0001)data in Zenodo doi:10.5281/zenodo.17307059 (per-cell rheobase, Figure 1F sheet); raw recordings in Zenodo doi:10.5281/zenodo.17260198
dSPN somatic excitability (rheobase) rises after the 6-OHDA lesion and falls in the LID off-state.
On the paper's table, rheobase 120 pA after the lesion against 220 pA in controls (P = 0.000295) and 200 pA in the off-state against 120 pA (P = 9.54e-05). The paper reports P < 0.0001 for both.
How the test differed from the paper’s method
- Tested on the paper's per-cell table; the raw recordings in Zenodo doi:10.5281/zenodo.17260198 were not reanalysed.
ReproducedFigure 1I; Results, first section (P = 0.824 and 0.905)data in Zenodo doi:10.5281/zenodo.17307059 (Figure 1I sheet)
The dSPN dendritic excitability index is not changed by the 6-OHDA lesion or in the off-state.
On the paper's table, P = 0.82 and 0.903 (reported 0.824 and 0.905).
How the test differed from the paper’s method
- Tested on the paper's table, not the raw line scans.
ReproducedFigure 3D; Results, second section (both P = 0.002)data in Zenodo doi:10.5281/zenodo.17307059 (Figure 3D sheet)
iSPN somatic excitability is lowered by the 6-OHDA lesion and restored in the LID off-state.
On the paper's table, rheobase 200 pA after the lesion against 120 pA in controls (P = 0.000401) and 130 pA in the off-state (P = 0.000608); reported P = 0.002 for both.
How the test differed from the paper’s method
- Tested on the paper's table.
ReproducedFigure 3F; Results, second section (P = 0.0327 and 0.0220)data in Zenodo doi:10.5281/zenodo.17307059 (Figure 3F sheet)
The iSPN dendritic excitability index rises after the lesion and stays raised in the off-state.
On the paper's table, 0.516 after the lesion and 0.519 off-state against 0.405 in controls (P = 0.0348 and 0.0242; reported 0.0327 and 0.0220).
How the test differed from the paper’s method
- Tested on the paper's table.
ReproducedFigure 7E (P = 0.0098 and 0.910, Wilcoxon)data in Zenodo doi:10.5281/zenodo.17307059 (Figure 7E sheet); raw line scans in Zenodo doi:10.5281/zenodo.17260198
Oxotremorine-M increases bAP invasion of iSPN dendrites in wild-type but not in CDGI KO mice.
On the paper's table, wild type 8 of 10 increase, Wilcoxon P = 0.009766 (reported 0.0098); KO 4 of 12 increase, P = 0.4697 (reported 0.910). Pairs are formed by the table's experiment number (printed); an unpaired Mann-Whitney test gives 0.885 for KO and 0.0539 for wild type, so neither test gives the reported 0.910.
How the test differed from the paper’s method
- Tested on the paper's table; the oxo-M line scans are not in the dandiset.
ReproducedFigure 8A (P = 0.0092 in the text; the legend marks P < 0.05)data in Zenodo doi:10.5281/zenodo.17307059 (Figure 8A sheet)
Levodopa induces more contralateral rotations in CDGI KO mice than in wild type at the fifth dose.
On the paper's table, KO 8.5 against wild type 4.25 rotations (10 and 12 mice), P = 0.012 (the text reports 0.0092, the legend P < 0.05).
How the test differed from the paper’s method
- Tested on the paper's table; the dandiset holds rotation videos for 7 CDGI-study mice without counts.
ReproducedFigure 10A (P = 0.0056)data in Zenodo doi:10.5281/zenodo.17307059 (Figure 10A sheet)
Levodopa induces more contralateral rotations in mice lacking M1Rs in iSPNs.
On the paper's table, 8.5 with M1R deletion against 6.0 in controls, P = 0.00782 (reported 0.0056).
How the test differed from the paper’s method
- Tested on the paper's table.
ReproducedFigures 10D to 10F; Results, fifth sectiondata in Zenodo doi:10.5281/zenodo.17307059 (Figure 10E and 10F sheets); raw ANY-maze data in Zenodo doi:10.5281/zenodo.17260198
In MCI-Park mice, a low dose of levodopa increases locomotion profoundly only when M1Rs are deleted from the striatum; M1R deletion alone does not.
On the paper's tables, MCI-Park against control distance 4.678 against 10.35 m (P = 1.05e-05), time mobile P = 6.97e-06; M1R deletion alone P = 0.628 and 0.467; levodopa with deletion against levodopa alone 28.09 against 6.52 m (P = 0.000332) and 276.4 against 127.45 s (P = 0.000567).
How the test differed from the paper’s method
- Tested on the paper's tables; the open-field data are not in the dandiset.

Not tested in a notebook 15

9 other, 6 methods underspecified

BlockedFigures 2G and 2H (P = 0.0003, Mann-Whitney)· Other
The amplitude of Sr2+-oEPSCs evoked from cortical afferents is larger in on-state than in off-state dSPNs.
The dandiset holds one cell per mouse, 3 off-state and 4 on-state dSPNs of the paper's 10 and 8. With 3 against 4 cells the smallest attainable two-sided Mann-Whitney P is 0.057, so the paper's test cannot reach P < 0.05. The per-cell values are shown under link-sr-cells; with the detector here the on-state amplitudes are all above the off-state ones (P = 0.057).
BlockedFigure 2I (P = 0.127)· Other
The frequency of Sr2+-oEPSCs in dSPNs does not differ between states.
Same 3 against 4 cells as fig2h; the test cannot detect a difference at P < 0.05 whatever the data, so the claim of absence cannot be judged. The frequencies are shown under link-sr-cells (P = 0.229).
BlockedFigures 2A to 2C· Methods underspecified
dSPN spine density falls in the off-state, and mushroom spines are more common in the on-state than in the off-state.
The dandiset holds the two-photon z-stacks of dSPN dendrites (off- and on-state) but no spine counts; none of the 86 spine files has a processing module or analysis entry. The paper deconvolved them in AutoQuant X3 and counted spines semi-automatically in NeuronStudio with manual classification of mushroom spines, a procedure that cannot be repeated from its description (also not runnable here, AutoQuant being commercial software). No control or 6-OHDA stacks for dSPNs were found. The per-cell densities are in the paper's Zenodo tables.
BlockedFigures 4F and 4G (P = 0.0003)· Other
The amplitude of Sr2+-oEPSCs is smaller in on-state than in off-state iSPNs.
One cell per mouse, 3 off-state and 4 on-state iSPNs of the paper's 7 and 8; the smallest attainable P is 0.057. With the detector here the on-state amplitudes are not all below the off-state ones (P = 0.229), while the paper's own per-cell values for these cells are (P = 0.057); shown under link-sr-cells.
BlockedFigure 4H (P = 0.23)· Other
The frequency of Sr2+-oEPSCs in iSPNs does not differ between states.
Same 3 against 4 cells as fig4g; the claim of absence cannot be judged by a test that cannot reach P < 0.05.
BlockedFigures 4A to 4C· Methods underspecified
Apparent iSPN spine density (2PLSM) falls after the lesion, returns in the off-state and falls in the on-state, in total and mushroom spines.
Two-photon z-stacks of iSPN dendrites are in the dandiset (off- and on-state, CDGI KO, M1R antagonist, M1R deletion) but no counts; counting needs AutoQuant deconvolution and semi-automatic NeuronStudio reconstruction with manual checks, which the paper does not describe well enough to repeat. The control and 6-OHDA stacks the lesion part needs are not in the dandiset (data_missing); the off- and on-state part is blocked by the counting alone.
BlockedFigures 4I to 4K; Results, second section· Methods underspecified
Confocal spine density of iSPN proximal dendrites is higher than the 2PLSM estimate (median 2.084 against 1.243 spines per um), falls after the lesion, rises modestly in the off-state and falls in the on-state.
Eleven confocal files of sparsely labelled iSPN dendrites (3 control, 3 6-OHDA, 3 off and 2 on) are in the dandiset, of the paper's 87 dendrites, with no counts. Counting used Imaris 10 with trained pixel classification and manual correction, which cannot be repeated from its description (and Imaris is commercial software).
BlockedFigure 5F (P < 0.0001)· Other
Evoked ACh release is markedly elevated in 6-OHDA-lesioned striatum compared with unlesioned striatum.
3 unlesioned and 3 6-OHDA mice, one region each; the smallest attainable P for 3 against 3 is 0.10. The values (unlesioned 0.089 to 0.113, 6-OHDA 0.179 to 0.269) are shown under link-grab-rois.
BlockedFigure 5F (P = 0.0005 and 0.0034)· Other
In unlesioned striatum sulpiride increases and quinpirole suppresses evoked ACh release.
3 unlesioned mice; a paired Wilcoxon test on 3 pairs cannot reach P < 0.05 (smallest 0.25). In all three, quinpirole lowers and sulpiride raises the area (shown under link-grab-rois).
BlockedFigure 5F (P = 0.002, 0.001; sulpiride P = 0.5566)· Other
Dopamine (50 nM) strongly suppresses evoked ACh release in 6-OHDA-lesioned and off-state striatum, and sulpiride has no effect after the lesion.
3 6-OHDA and 5 off-state mice; paired tests on 3 or 5 pairs cannot reach P < 0.05 (smallest 0.25 and 0.0625). Dopamine lowers the area in all 8 mice (shown under link-grab-rois); sulpiride after the lesion raises it in two of three.
BlockedFigures 6E and 6F (P = 0.0003)· Methods underspecified
M1R antagonism prevents the off-state elevation of apparent iSPN spine density.
Z-stacks are in the dandiset without counts (see fig4bc-ispn-spines).
BlockedFigures 7G and 7H (P = 0.613)· Methods underspecified
The off-state increase in apparent iSPN spine density is absent in CDGI KO mice.
Z-stacks are in the dandiset without counts (see fig4bc-ispn-spines).
BlockedFigures 8B and 8C (repeated-measures two-way ANOVA, group P < 0.001 to 0.002)· Othernames its codes from outside the dandiset
Axial, limb, orolingual and total AIMs are less severe in CDGI KO mice than in wild type.
The dandiset holds AIM tables for 5 of the paper's 23 Figure 8 mice (4 KO, 1 wild type) and 2 mice not in the paper; with one wild-type mouse the paper's repeated-measures ANOVA cannot be run. The dandiset's genotype labels contradict each other, and the session totals of these mice differ from the paper's in 20 of 25 sessions (link-aim-mice, not reproduced).
BlockedFigures 9E and 9F (P = 0.0005)· Methods underspecified
Deletion of M1Rs from iSPNs blunts the off-state increase in apparent spine density.
Z-stacks are in the dandiset without counts (see fig4bc-ispn-spines).
BlockedFigure 10B (repeated-measures two-way ANOVA, group P < 0.001 to 0.0015)· Othernames its codes from outside the dandiset
AIMs are attenuated by deletion of M1Rs in iSPNs.
The dandiset holds AIM tables for 2 of the paper's 21 Figure 10 mice, one control (5844) and one M1R deletion (5846), whose totals equal the paper's; one mouse per group cannot be tested. Mouse 5846 has lower totals than 5844 in every session.

Findings about the data

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

Data missingThe dandiset holds no patch-clamp recordings from unlesioned control or 6-OHDA-lesioned mice, which make up the control and 6-OHDA groups of Figures 1E, 1F, 1I, 3C, 3D and 3F (10, 12, 11 and 9 dSPNs; 21, 11, 14 and 9 iSPNs), nor the oxo-M line scans of Figure 7E or the open-field data of Figure 10. The paper's raw data on Zenodo (doi:10.5281/zenodo.17260198) list folders for all of these.
Selection not documentedThe Sr2+-oEPSC files hold one cell per mouse (14 of the paper's 33 cells), the GRAB-ACh files one region per mouse (11 of 34 regions) and the AIM tables 7 of the paper's 44 mice plus two mice (4124, 5871) not in the paper. The dandiset does not say that it holds a subset or how the cells, regions and mice were chosen, and with these numbers the paper's tests cannot reach P < 0.05 for most comparisons.
Metadata errorSession names state a drug (D1RaSch, D2RaSul) for files that also hold baseline on-state sweeps. 11 cells in such files have a baseline condition; 7 of them were also recorded with the drug and 4 are baseline only (dSPN 20190507 cell 1, iSPN 20190408 cell 1, 20190409 cell 1 and 20190508 cell 2). The condition of each sweep is only in the RecordingsIndexTable column condition_subfolder; grouping by session name puts baseline cells in the drug groups.
Metadata errorThe genotypes of the CDGI behaviour mice contradict each other. Subject genotype is Wild-type CDGI and every session name says WT for all of them; the AIM table's genotype column says CDGI Knockout, Wild Type or unknown, changing between sessions of one animal; the video files of mice 1945, 2519, 2587, 2828 and 6572 say CDGI KO. The paper lists 2587 as wild type and the others as KO.
OtherThe AIM session totals of the five Figure 8 mice in the dandiset differ from the paper's table in 20 of 25 sessions (mouse 1945 session 1, 33.5 against 27.0), while the two Figure 10 mice agree in all sessions. Some dandiset sessions have 4 time points and others 6.
Metadata errorThree dendritic site series hold six trials, two sites under one name, while the cell has no series of the other compartment with that number (iSPN 20160526 cell 3 Distal1, iSPN 20160608 cell 1 Proximal1, dSPN 20170204 cell 1 Proximal1); their first and last three trials differ in baseline and area. Split, they give the paper's values for these cells. One series holds a single trial (iSPN 20160524 cell 2 Proximal1), one two and one four.
Data missingTwo dendritic cells lack the sites the paper's values need. dSPN on+SCH 20190411 cell 1 has only its second pair of sites, which gives 0.584 against the paper's 0.228; with the paper's value the SCH test gives the paper's P (0.0133), without it P = 0.066. iSPN on+sul 20190508 cell 3 has only a distal site; with the paper's 0.217 the sulpiride test gives the paper's P (0.0545), without it P = 0.0097. Under the main basal-ratio rule these two cells decide fig1i-dspn-dendritic-sch-lower and fig3f-ispn-dendritic-sul-no-change; under the stricter rule (0.8 to 1.25) the sulpiride test gives P = 0.0663 without the cell. Reading the gap as data missing is an inference from the recovered P values, as the paper does not list each cell's sites.
Description missingThe dandiset holds the raw spine image stacks and the rotation videos but no spine counts or rotation counts (none of the 86 spine files has a processing module or analysis entry), the measurements behind Figures 2B, 2C, 4B, 4C, 4K, 6F, 7H, 8A, 9F and 10A. They are only in the paper's Zenodo tables.
Metadata errorThe stimulus series of every dendritic sweep (CurrentClampSeries_CellN_Dendritic_Stimulus) is all zero, though the three spikes per sweep show the 2 nA injections were delivered; and the index table gives no kymograph slice for 53 of 997 dendritic sweeps.
Metadata errorIn the Sr2+-oEPSC files the light-pulse OptogeneticSeries is all zero in 69 of 140 sweeps, and the intracellular recordings table references no stimulus (its stimulus rows are empty). The pulse time (0.02 s) is only in the optogenetic epochs table.
Metadata errorThe GRAB-ACh background reference images are described as taken at zero laser power, but their mean (381 to 525) is above the signal (F0 179 to 355), so they cannot be the PMT background the Methods subtract.
Metadata errorThe files cite the bioRxiv preprint (related_publications) and describe the behaviour data with the preprint's figure numbers ("Figure 7J" for the CDGI AIM scores, "Figure 8" for the M1R study), which are Figures 8 and 10 in the published paper the dandiset names.
Identifier missingPatch-clamp subjects are named by recording date (for example Subject20160523LIDOFFeGFP and SubjectRecordedAt20160523000000 for the same day), with no animal identifier, so recordings and spine stacks of one mouse cannot be linked, and the archive has 185 subject folders.
Paper inconsistentRecomputed on the paper's own per-cell tables, some reported P values differ; the oxo-M test in CDGI KO gives P = 0.47 where the paper reports 0.910, and the rotation test of Figure 8A gives 0.012 where the text reports 0.0092. Others agree closely (0.009766 against 0.0098 for oxo-M in wild type).
Other18 somatic cells miss one or more current steps between 20 and 300 pA and 14 repeat a step; spike counts for these cells cannot be complete.

Notebooks

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

Reproduction State-dependent modulation of spiny projection neurons in levodopa-induced dyskinesia (Zhai et al. 2025)

Tests the findings of Zhai, Cui, Wokosin, Sun, Tkatch, Crittenden, Graybiel and Surmeier (2025) on dandiset 001538. It measures somatic excitability (rheobase and spike counts) and the dendritic excitability index of dSPNs and iSPNs in the LID off- and on-states and under D1R, D2R and M1R antagonists, CDGI deletion and M1R deletion, and evoked ACh release with GRAB-ACh3.0. It links the recordings to the paper's per-cell tables on Zenodo. The Sr2+-oEPSC, ACh and AIM data hold too few cells or mice for most of the paper's tests, and the spine data are raw stacks only. All files

Reproducing Zhai et al. (2025) from dandiset 001538
reproduce_zhai_2025.ipynbExecuted, with outputs · Source

Verification

Round 1
2026-10-18
Agreed with 44 of 45 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: The executed notebook of the first run with the conclusion cells and the summary removed, the helper module and the claims file.
- fig1i-dspn-dendritic-sch-lower: the verifier’s outcome was “Not reproduced”. P = 0.066 (paper 0.0133). The SCH median is 0.419 against the paper's 0.338; one SCH cell differs 2.6-fold from the paper and may drive this. Replacing each of the top five SCH values in turn with value/2.559 gives P = 0.014 to 0.041, so the claim may fail because of one computed index, not the data. The stricter 0.8 to 1.25 basal-ratio variant gives P = 0.52.
Round 2
2026-10-19Agreed with 45 of 45 outcomes. Independent agent run by CatalystNeuro (same harness, separate context, did not write the notebook). Reviewed: Round 2. The full executed notebook of the revised run, with the conclusions and the summary, the helper module, the claims file and the attempt record.

Method differences

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

Tested on the paper's table.fig3-ispn-lesion-and-off-somatic fig3-ispn-lesion-dendritic-up fig10a-m1r-rotations
The paper gives no test; its default Mann-Whitney test on rheobase was used.fig6c-m1r-antag-somatic-unchanged fig9d-m1r-crispr-somatic-unchanged
The paper's spike counts come from its script run on Prairie View exports; the differences of 1 to 24 spikes may come from the export or from cells whose steps are missing or repeated in the files (18 cells miss a step, 14 repeat one).link-somatic-cells
Outside Figure 6D the paper's table has no cell identifiers, so cells are matched by order, an assumption supported by the somatic link.link-dendritic-cells
The background constants of the paper's script (55 red, 161 green) are used for every session, as the files carry no per-session background.link-dendritic-cells
Three six-trial series are split into their first and last three trials, the half with the smaller area taken as distal, a choice made here from the data; the sites as labelled are a variant.link-dendritic-cells
Events are found with a threshold detector written here (low-pass 1 kHz, five robust SD, local baseline); the paper used TaroTools with visual verification, which cannot be repeated.link-sr-cells
The stimulus time is taken from the trial table (3 s after the trial start in six files), where the paper's script fixes 10 s.link-grab-rois
The paper's session total is taken to be the sum over the session's time points; the Figure 8 mice have 4 time points in some dandiset sessions and 6 in others.link-aim-mice
The paper shows F-I curves without a test; the summed count and its test were chosen here.fig1e-dspn-fi-on-higher
Background constants from the paper's script; basal-ratio rule (0.5 to 2) chosen here, dropping no pair; one six-trial series split into two sites.fig1i-dspn-dendritic-on-higher
Matching the SCH cells to the paper's rows by order is an assumption (link-dendritic-cells).fig1i-dspn-dendritic-sch-lower
The summed count and its test were chosen here.fig3c-ispn-fi-on-lower
One on-state cell gets its index only from splitting a six-trial series into two sites.fig3f-ispn-dendritic-on-lower
The Methods keep pairs with similar G0/R0 without a threshold; the 0.5 to 2 rule chosen here drops no pair.fig3f-ispn-dendritic-on-lower
One sulpiride cell has no index here (only a distal site).fig3f-ispn-dendritic-sul-no-change
One region per mouse, 8 of the paper's 24 regions in these two groups.fig5f-ach-off-elevated
Stimulus time from the trial table.fig5f-ach-off-elevated
One region per mouse, 8 of the paper's 21 regions in these two groups.fig5f-ach-off-like-6ohda
The test cannot find any difference short of complete separation, so this claim of absence passes with little power.fig5f-ach-off-like-6ohda
The paper shows F-I curves without a test; a Mann-Whitney test of rheobase was chosen here.fig7c-cdgi-ko-somatic-oscillation
One KO off-state cell gets its index only from splitting a six-trial series into two sites.fig7f-cdgi-ko-dendritic-unchanged
Tested on the paper's per-cell table; the raw recordings in Zenodo doi:10.5281/zenodo.17260198 were not reanalysed.fig1-dspn-lesion-and-off-somatic
Tested on the paper's table, not the raw line scans.fig1-dspn-lesion-dendritic-unchanged
Tested on the paper's table; the oxo-M line scans are not in the dandiset.fig7e-oxom-cdgi
Tested on the paper's table; the dandiset holds rotation videos for 7 CDGI-study mice without counts.fig8a-cdgi-rotations
Tested on the paper's tables; the open-field data are not in the dandiset.fig10ef-open-field

Provenance

Attempt record: 001538-zhai-2025-01
Paper: State-dependent modulation of spiny projection neurons controls levodopa-induced dyskinesia in a mouse model of Parkinson’s disease
Date: 2026-10-18
Made by: An agent, run by CatalystNeuro
Dandiset version: 0.260527.1302
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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