Reporting Checklist for Nature Neuroscience

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1 Corresponing Author: Manuscript Number: Manuscript Type: Kathryn V. Anerson an SongHai Shi NNA4806B Article Reporting Checklist for Nature Neuroscience # Main Figures: 7 # Supplementary Figures: 1 # Supplementary Tables: 0 # Supplementary Vieos: 0 This checklist is use to ensure goo reporting stanars an to improve the reproucibility of publishe results. For more information, please rea Reporting Life Sciences Research. Please e that in the event of publication, it is manatory that authors inclue all relevant methoological an statistical information in the manuscript. Statistics reporting, by figure example example Please specify the following information for each panel reporting quantitative ata, an where each item is reporte (section, e.g. Results, & paragraph number). Each figure legen shoul ieally contain an exact sample size (n) for each experimental group/conition, where n is an exact number an a range, a clear efinition of how n is efine (for example x from x slices from x animals from x litters, collecte over x ays), a escription of the statistical use, the results of the s, any escriptive statistics an clearly efine error bars if applicable. For any experiments using custom statistics, please inicate the use an stats obtaine for each experiment. Each figure legen shoul inclue a statement of how many times the experiment shown was replicate in the lab; the etails of sample collection shoul be sufficiently clear so that the replicability of the experiment is obvious to the reaer. For experiments reporte in the text but in the figures, please use the paragraph number instea of the figure number. e: Mean an stanar eviation are appropriate on small samples, an plotting inepenent ata points is usually more informative. When technical replicates are reporte, error an significance measures reflect the experimental variability an the variability of the biological process; it is misleaing to state this clearly. FIGURE NUMBER 1a results, para 6 TEST USED WHICH TEST? oneway ANOVA legen Results para 6 EXACT VALUE 9, 9, 10, 1 n DEFINED? mice from at least 3 litters/group 1 slices from 10 mice s para 8 Results para 6 DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? error bars are mean / SEM error bars are mean / SEM legen Results para 6 P VALUE EXACT VALUE p = p = 0.0 legen Results para 6 DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE F(3, 36) = 2.97 t(28) = legen Results para 6 1

2 FIGURE NUMBER 2b 2 TEST USED WHICH TEST? 2e 2h 2i s para s para EXACT VALUE P1: 4,4,4 P14: 3, n DEFINED? slices from ifferent slices from ifferent slices from ifferent slices from ifferent legen legen DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? Mean / S.D. Mean / S.D. Mean / S.D. Mean / S.D. Mean / S.D. Fig P VALUE EXACT VALUE (P1) (**)p= (P1) p= (P14) p= (Cux1)(**) p= e 007 (Cux1) p= (CTIP2)(**) p= e 00 p=0.013 (Cux1)(**) p= (Cux1) p= p= p= (Cux1) p= p= (Cux1) p= p= Fig Fig Fig DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE (P1) (**) t= f=6 (P1) (n.s) t= f=6 (P14) t= f= (Cux1)(**) t=12.4 f=10 (Cux1)(n.s) t=1.244 f=10 (CTIP2)(**) t=7.96 f=10 t=2.213 f=10 (Cux1)(**) t= f=10 (Cux1) t= f=10 t= f=10 t= f=10 (Cux1) t= f=6 t=1.341 f=6 (Cux1) t= f=6.0 t= f=6 inclue inclue inclue inclue inclue 2

3 3b 3 4c c,4,,4, 10, 91, 143 EGFP;PAX6, Mean / S.D. Mean / S.D. none Mean / S.D. (WT v Sas4) (all **) black: p= e 00 Re: p= Blue: p= e (WT v Sas4p3) black (n.s): p= Re(**): p= e 008 p= e (Sas4 v Sas4p3) black (**): p= e Re(**): p= e Blue: p=0.190 (WT v Sas4) black (**): p= Re: p= p= (WT v Sas4p3) Black (n.s): p= Re(**): p= e 008 p=9.9941e 00 (Sas4 v Sas4p3) p= Re(**): p=9.2967e 007 Blue: p= (**)black p= e 00 (**)re p= e p= Fig Fig (WT v Sas4) (all **) black: t= f=7 Re: t= f=7 Blue: t= f=7 (WT v Sas4p3) black (n.s): t= f=8 Re(**): t= f=8 t= f=8 (Sas4 v Sas4p3) black (**): t= f=7 Re(**): t= f=7 Blue: t= f=7 (WT v Sas4) black(**): t= f=7 Re: t= f=7 t= f=7 (WT v Sas4p3) black (n.s): t= f=8 Re(**): t= f=8 t= f=8 (Sas4 v Sas4p3) black (**): t= f=7 Re(**): t= f=7 Blue: t= f=7 (**)black t= f=8 (**)re t= f=8 t= f=8 inclue inclue inclue 3

4 e 6b 6 7b (left) 7b (right ) s3c s3e, 461 from 3, from 3, 690 1,397 PAX6 2,027 PAX6 from PAX6 ;BrU ;EU 449 PAX6 ;BrU ;EU from 4 from from from from,4,4 Mean / S.D. Mean / S.D. of Mean / S.D. of Mean / S.D. of Mean / S.D. of Mean / S.D. Mean / S.D. (**)black p= e 00 (**)re p= e 007 p= (VZ Surface) both (**) p= e 00 (ExtraVZ) both(**) p= VZ Surface (Two Foci)(**) p= e 007 (One Foci)(**) p= e (No Foci)(**) p= e 00 ExtraVZ (Two Foci)(**) p= e 008 (One Foci)(**) p= (No Foci)(**) p= p=0.309 (**) both p= black p= re p= p= black p= re p= p= Fig (**)black t=9.942 f=8 (**)re t=1.211 f=8 t= f=8 (VZ Surface) both (**) t= f=4 (ExtraVZ) both(**) t= f=4 VZ Surface (Two Foci)(**) t= f=4 (One Foci)(**) t= f=4 (No Foci)(**) t= f=4 ExtraVZ (Two Foci)(**) t=10.33 f=4 (One Foci)(**) t= f=4 (No Foci)(**) t= f=4 (n.s) t=1.029 f= (**) both t=9.141 f= black t= f=7 re t= f=7 t= f=7 black t= f=7 re t= f=7 t= f=7 inclue inclue inclue inclue inclue inclue inclue 4

5 s3g sa sc s8b s8 s9b s9 s9e s10b,4 3,10 CUX1 from 3,062 CUX1 from from 3,3 400 p3 391 p3 1,388 PAX6 1,484 PAX6 1,39 PAX6 1,11 PAX6 23 PAX6 ;BLBP from from from from 4,4,4 s s s s s s Mean / S.D. Mean / S.D. of Mean / S.D. black p= re p= p= (Bin 4) (**) p=0.00 FOXP2 p= SATB2 p= black t= f=7 re t= f=7 t= f=7 t=3.762 f=8 FOXP2 t= f=4 SATB2 t= f=4 Mean / S.D. Mean / S.D. Mean / S.D. of (S.D.=0 for all bars because 100% PAX6 were SOX2) Mean / S.D. of n.s. WT VZ vs Sas4p3 VZ p= WT VZ vs Sas4p3 evz p= Sas4p3 VZ vs Sas4p3 evz p=0.332 Results section because all values were 100% WT VZ vs Sas4p3 VZ t= f=4 WT VZ vs Sas4p3 evz t=2.29 f=4 Sas4p3 VZ vs Sas4p3 evz t=1.101 f=4 inclue inclue inclue inclue inclue inclue none Mean / S.D. (**) p= e p=0.784 (**) t=19.96 f=6 t=0.874 f=6 inclue

6 s10 s10e 4,3,4 4,3,4 s s Mean / S.D. Mean / S.D. (WT v Sas4) p= Re : p=0.19 Blue (**) : p= (WT v Sas4p3) Black (n.s): p= Re(**): p= p= (Sas4 v Sas4p3) p= Re(**): p= Blue(*): p= (WT v Sas4) p= Re : p= Blue (**) : p= (WT v Sas4p3) Black (n.s): p= Re(**): p= p=0.000 (Sas4 v Sas4p3) p= Re(**): p= p= (WT v Sas4) t=12.73 f= Re : t=1.62 f= Blue (**): t= f= (WT v Sas4p3) Black (n.s): t=0.148 f=6 Re(**): t=11.1 f=6 t= f=6 (Sas4 v Sas4p3) t=12.73 f= Re(**): t=9.66 f= Blue (*): t=2.769 f= (WT v Sas4) t=12.70 f= Re : t=1.608 f= Blue (**): t=11.98 f= (WT v Sas4p3) Black (n.s): t=1.026 f=6 Re(**): t=6.268 f=6 t=6.700 f=6 (Sas4 v Sas4p3) t=6.82 f= Re(**): t=.876 f= Blue (**): t=4.944 f= inclue inclue 6

7 s11b s12b s13b s13c s16b 4,4,2,4 iniviual areas 6, 70, 40 DiI; PAX6 3,3 1,19 BrU 1,492 BrU from from s16 112, 61 Mitotic s1b 238 BrU ;EU 262 BrU ;EU from legens legens legens legens legens legens legens Mean / S.D. (Top left) (E14.) p= (E1.) p= (Bottom left) (E12.) p= (E13.) p= (E14.) p= (E1.) p= (Top right) (E14.) p= (E1.) p= (Bottom right) (E12.) p= (E13.) p= e (E14.) p= (E1.) p= (top left) (E14.) t= f=2 E1. t= f=6 (Bottom left) (E12.) t= f=6 (E13.) t=.0384 f=6 (E14.) t= f=2 (E1.) t= f=6 (Top right) (E14.) t= f=2 E1. t= f=6 (Bottom right) (E12.) t= f=6 (E13.) t= f=6 (E14.) t=1.846 f=2 (E1.) t= f=6 inclue none Mean / S.D. Mean / S.D. of Mean / S.D. of (*) p= p= p= (*) t=4.388 f=4 t=1.47 f=4 t=1.297 f=4 inclue inclue inclue none Mean / S.D. of (**) p= (**) t=16.32 f=4 inclue 7

8 s1c 199 BrU ;EU ;BLBP 199 BrU ;EU ;BLBP Representative figures from legens 1. Are any representative images shown (incluing Western blots an immunohistochemistry/staining) in the paper? If so, what figure(s)? 2. For each representative image, is there a clear statement of how many times this experiment was successfully repeate an a iscussion of any limitations in repeatability? If so, where is this reporte (section, paragraph #)? Statistics an general methos 1. Is there a justification of the sample size? If so, how was it justifie? Even if no sample size calculation was performe, authors shoul report why the sample size is aequate to measure their effect size. 2. Are statistical s justifie as appropriate for every figure? a. If there is a section summarizing the statistical methos in the methos, is the statistical for each experiment clearly efine? b. Do the ata meet the assumptions of the specific statistical you chose (e.g. normality for a parametric )? Where is this escribe (section, paragraph #)? Mean / S.D. of (**) both p= (**) both t=22.2 f=4 All images are representative an most are accompanie by quantitative analysis. The following figures contain only representative images: Fig 1cj, Fig 4a, Fig a inclue sfig 1, sfig 2, sfig 3a&h, sfig 4, sfig 6, sfig 7, sfig 13a, sfig 14, sfig 16b&c No, but all were representative of more than 23 iniviual experiments. Sample size is generally justifie base on statistical analysis, an previous publications on similar topics (state in s section). Yes, s. Yes, graph Yes, all meet criteria of p<0.0 in t. 8

9 c. Is there any estimate of variance within each group of ata? Is the variance similar between groups that are being statistically compare? Where is this escribe (section, paragraph #)? Yes, all bar graphs are represente as mean / stanar eviation, as escribe in Figure s an s.. Are s specifie as one or twosie? Twosie, state in s paragraph. e. Are there ajustments for multiple comparisons? No 3. Are criteria for excluing ata points reporte? Was this criterion establishe prior to ata collection? Where is this escribe (section, paragraph #)? 4. Define the metho of ranomization use to assign subjects (or samples) to the experimental groups an to collect an process ata. If no ranomization was use, state so. Where oes this appear (section, paragraph #)?. Is a statement of the extent to which investigator knew the group allocation uring the experiment an in assessing outcome inclue? If no blining was one, state so. 6. For experiments in live vertebrates, is a statement of compliance with ethical guielines/regulations inclue? 7. Is the species of the animals use reporte? 8. Is the strain of the animals (incluing backgroun strains of KO/ transgenic animals use) reporte? 9. Is the sex of the animals/subjects use reporte? 10. Is the age of the animals/subjects reporte? No ata points were exclue as state in s. No ranomization was use as state in s. No blining experiment was one, because all reporte ifferences amongst groups were clear. This is state in the methos section. Yes, in s section, paragraph 1. Yes, in s section, paragraph 1. Mice are use. Yes, in s section, paragraph 1. No. Yes, in Figures an Figure s for all figures. 11. For animals house in a vivarium, is the light/ark cycle reporte? No 9

10 12. For animals house in a vivarium, is the housing group (i.e. number of animals per cage) reporte? 13. For behavioral experiments, is the time of ay reporte (e.g. light or ark cycle)? 14. Is the previous history of the animals/subjects (e.g. prior rug aministration, surgery, behavioral ing) reporte? a. If multiple behavioral s were conucte in the same group of animals, is this reporte? 1. If any animals/subjects were exclue from analysis, is this reporte? Reagents a. How were the criteria for exclusion efine? Where is this escribe (section, paragraph #)? b. Specify reasons for any iscrepancy between the number of animals at the beginning an en of the stuy. Where is this escribe (section, paragraph #)? 1. Have antiboies been valiate for use in the system uner stuy (assay an species)? a. Is antiboy catalog number given? Where oes this appear (section, paragraph #)? b. Where were the valiation ata reporte (citation, supplementary information, Antiboypeia)? Where oes this appear (section, paragraph #)? 2. If cell lines were use to reflect the properties of a particular tissue or isease state, is their source ientifie? No No animals were exclue, as state in the s section. Yes, by the previous publications an the venors. Specific noncommercial antiboies are referre in s section. Yes, along with the ilution factor use: in the s section, paragraph 3. Specific noncommercial antiboies are cite in s section, paragraph 3. 10

11 a. Were they recently authenticate? Where is this information reporte (section, paragraph #)? Data eposition Data eposition in a public repository is manatory for: a. Protein, DNA an RNA sequences b. Macromolecular structures c. Crystallographic ata for small molecules. Microarray ata Deposition is strongly recommene for many other atasets for which structure public repositories exist; more etails on our ata policy are available here. We encourage the provision of other source ata in supplementary information or in unstructure repositories such as Figshare an Drya. 1. Are accession coes for eposit ates provie? Computer coe/software Any custom algorithm/software that is central to the methos must be supplie by the authors in a usable an reaable form for reaers at the time of publication. However, referees may ask for this information at any time uring the review process. 1. Ientify all custom software or scripts that were require to conuct the stuy an where in the proceures each was use. 2. Is computer source coe/software provie with the paper or eposite in a public repository? Inicate in what form this is provie or how it can be obtaine. Human subjects 1. Which IRB approve the protocol? Where is this state (section, paragraph #)? 2. Is emographic information on all subjects provie? 3. Is the number of human subjects, their age an sex clearly efine? 4. Are the inclusion an exclusion criteria (if any) clearly specifie? 11

12 . How well were the groups matche? Where is this information escribe (section, paragraph #)? 6. Is a statement inclue confirming that informe consent was obtaine from all subjects? 7. For publication of patient photos, is a statement inclue confirming that consent to publish was obtaine? fmri stuies For papers reporting functional imaging (fmri) results please ensure that these minimal reporting guielines are met an that all this information is clearly provie in the methos: 1. Were any subjects scanne but then rejecte for the analysis after the ata was collecte? a. If yes, is the number rejecte an reasons for rejection escribe? 2. Is the number of blocks, trials or experimental units per session an/ or subjects specifie? 3. Is the length of each trial an interval between trials specifie? 4. Is a blocke, eventrelate, or mixe esign being use? If applicable, please specify the block length or how the eventrelate or mixe esign was optimize.. Is the task esign clearly escribe? 6. How was behavioral performance measure? 7. Is an ANOVA or factorial esign being use? 8. For ata acquisition, is a whole brain scan use? If, state area of acquisition. a. How was this region etermine? 12

13 9. Is the fiel strength (in Tesla) of the MRI system state? a. Is the pulse sequence type (graient/spin echo, EPI/spiral) state? b. Are the fielofview, matrix size, slice thickness, an TE/TR/ flip angle clearly state? 10. Are the software an specific parameters (moel/functions, smoothing kernel size if applicable, etc.) use for ata processing an preprocessing clearly state? 11. Is the coorinate space for the anatomical/functional imaging ata clearly efine as subject/native space or stanarize stereotaxic space, e.g., original Talairach, MNI30, ICBM12, etc? Where (section, paragraph #)? 12. If there was ata normalization/stanarization to a specific space template, are the type of transformation (linear vs. nonlinear) use an image types being transforme clearly escribe? Where (section, paragraph #)? 13. How were anatomical locations etermine, e.g., via an automate labeling algorithm (AAL), stanarize coorinate atabase (Talairach aemon), probabilistic atlases, etc.? 14. Were any aitional regressors (behavioral covariates, motion etc) use? 1. Is the contrast construction clearly efine? 16. Is a mixe/ranom effects or fixe inference use? a. If fixe effects inference use, is this justifie? 17. Were repeate measures use (multiple measurements per subject)? a. If so, are the metho to account for within subject correlation an the assumptions mae about variance clearly state? 18. If the threshol use for inference an visualization in figures varies, is this clearly state? 19. Are statistical inferences correcte for multiple comparisons? a. If, is this labele as uncorrecte? 13

14 20. Are the results base on an ROI (region of interest) analysis? a. If so, is the rationale clearly escribe? b. How were the ROI s efine (functional vs anatomical localization)? 21. Is there correction for multiple comparisons within each voxel? 22. For clusterwise significance, is the clusterefining threshol an the correcte significance level efine? Aitional comments Aitional Comments 14