Reporting Checklist for Nature Neuroscience

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1 Correspondg Author: Manuscript Number: Manuscript Type: Spencer Smith NNA48000A Article Reportg Checklist for Nature Neuroscience # Ma Figures: 6 # Supplementary Figures: 8 # Supplementary Tables: 1 # Supplementary Videos: 0 This checklist is used to ensure good reportg standards and to improve the reproducibility of published results. For more formation please read Reportg Life Sciences Research. Please note that the event of publication it is mandatory that authors clude all relevant methodological and statistical formation the manuscript. Statistics reportg by figure example example Please specify the followg formation for each panel reportg quantitative data and where each item is reported (section e.g. & paragraph number). Each figure legend should ideally conta an exact sample size (n) for each experi group/condition where n is an exact number and not a range a clear defition of how n is defed (for example x cells from x slices from x animals from x litters collected over x days) a description of the statistical test used the results of the tests any descriptive statistics and clearly defed error bars if applicable. For any experiments usg custom statistics please dicate the test used and stats obtaed for each experiment. Each figure legend should clude a statement of how many times the experiment shown was replicated the lab; the details of sample collection should be sufficiently clear so that the replicability of the experiment is obvious to the reader. For experiments reported the text but not the figures please use the paragraph number stead of the figure number. Note: Mean and standard deviation are not appropriate on small samples and plottg dependent data pots is usually more formative. When technical replicates are reported error and significance measures reflect the experi variability and not the variability of the biological process; it is misleadg not to state this clearly. FIGURE NUMBER 1a results para 6 TEST USED WHICH TEST? oneway ANOVA unpaired t test Fig. legend para 6 EXACT VALUE n DEFINED? mice from at least 3 litters/group 15 slices from 10 mice Methods para 8 para 6 DESCRIPTIVE STATS (AVERAGE VARIANCE) REPORTED? error bars are mean / SEM error bars are mean / SEM Fig. legend para 6 P VALUE EXACT VALUE p = p = Fig. legend para 6 DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE F(3 36) = 2.97 t(28) = Fig. legend para 6 1

2 FIGURE NUMBER 1 21 TEST USED WHICH TEST? Lear regression ANOVA & Tukey Kramer HSD 22 ANOVA 3 Lear regression 4 ranksum "Respo nse correla tions among "Early and latedevelo pg "Early and latedevelo pg "Visual respon ses at divid ual neuron resolut ion" "Devel opmen tal change s " EXACT VALUE n DEFINED? 22 mice P1314: n=11; P1516 n=13; P1718 n=12; P2036 (chronic experime nts) n=7 DR n=9; P40 n=13; Recovery n=9; P65 n=9 n=5 n = 266 LM neurons at P at P PM neurons at P at P36 mice mice pairwise comparisons cells "Respons e correlatio ns among "Early and latedevelop g "Early and latedevelop g "Visual response s at dividual neuron resolutio n" " DESCRIPTIVE STATS (AVERAGE VARIANCE) REPORTED? Pearson's R Result s "Resp onse correl ations amon g Fig 1 Supp Table 1 Mean and SEM Fig. 3 Mean and SEM Fig. 2 P VALUE EXACT VALUE Listed Supp Table 1 P < ; P = ; P = ; P = 0.036; P = 0.90; P = P = 0.028; P = 0.16; P = ; P = 0.39 Pearson's R Fig. 3 P = Mean and SEM Fig. 4 P<0.0001; P<0.0001; P<0.0001; P<0.0001;P<0. Supp Table 1 "Early and latedevelopi ng "Early and latedevelopi ng ; And details Methods "Visual response s at dividua l neuron resolutio n" Fig. 3 " DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE 2

3 5 ranksum 6 ranksum S1 S2 lear regression lear regression "Devel opmen tal change s orienta tion tung " "Devel opmen tal change s recepti ve field (RF) maps " Fig. S1 for 0.04 cycles/ deg P20: n= (V1LM PM); P36: n= (V1LMP M); for 0.32 cycles/ deg P20: n= (V1LMP M) P36: n= (V1 LM PM) P20: n= ON n= OFF for V1 LM and PM respectiv ely;at P36: n = ON subregio ns and n = OFF subregio ns 13 for V1 LM and PM respectiv ely n=52 maps 1 per mouse cells cells Fig. S2 22 mice mice orientatio n tung " receptive field (RF) maps " Cumulative histogram Mean and SEM Fig. 5 P=4e13 P=1e8P= P=0.04P= P=0.03 Mean and SEM Fig. 6 P< maps/mice Fig. S1 Pearson's R Fig. S1 "Respons e correlatio ns among Pearson's R Fig. S2 S3 no test Mean and SEM Fig. S3 S4 no test Mean and SEM Fig. S4 S5 no test Mean and SEM Fig. S5 orientati on tung " and Fig. 5 receptiv e field (RF) maps " 3

4 S6 ranksum S7 no test S8 no test "Devel opmen tal change s orienta tion tung " for 0.04 cycles/ deg P20: n= (V1LM PM); P36: n= (V1LMP M); for 0.32 cycles/ deg P20: n= (V1LMP M) P36: n= (V1 LM PM) P20: n= ON n= OFF for V1 LM and PM respectiv ely;at P36: n = ON subregio ns and n = OFF subregio ns 13 for V1 LM and PM respectiv ely P20: n= ON n= OFF for V1 LM and PM respectiv ely;at P36: n = ON subregio ns and n = OFF subregio ns 13 for V1 LM and PM respectiv ely cells cells cells orientatio n tung " receptive field (RF) maps " receptive field (RF) maps " Cumulative histogram Mean and SEM Box plots of data distributions Box plots of data distributions Fig. S6 Fig. S7 Fig. S8 P=0.0002; P=0.3; P=0.05; P=1; P=0.05; P=0.3 orientati on tung " and Fig. S6 4

5 T1 Lear regression "Respo nse correla tions among 22 mice Representative figures "Respons e correlatio ns among 1. Are any representative images shown (cludg Western blots and immunohistochemistry/stag) 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 repeated and a discussion of any limitations repeatability? If so where is this reported (section paragraph #)? Statistics and general methods 1. Is there a justification of the sample size? If so how was it justified? Where (section paragraph #)? Even if no sample size calculation was performed authors should report why the sample size is adequate to measure their effect size. 2. Are statistical tests justified as appropriate for every figure? Where (section paragraph #)? a. If there is a section summarizg the statistical methods the methods is the statistical test for each experiment clearly defed? b. Do the data meet the assumptions of the specific statistical test you chose (e.g. normality for a parametric test)? Where is this described (section paragraph #)? Pearson's R Supp. Table 1 Listed Supplementar y table 1 Supp. Table 1 Example data from is displayed Figs 1356 and 7. Yes. The locations of the exact Ns are listed the table above. Conclusions are based on quantitative analysis and statistics not on subjective impressions. Our key fdgs are supported by experiments that were each repeated at least 7 times (e.g. P20P36 data Fig. 4) and as many as 22 times (e.g. Fig. 3). These sample sizes were sufficient to yield P values << 0.05 most cases. Further creases sample sizes beyond this level might further reduce Pvalues but we are most terested effects large and reliable enough to be revealed by reasonable sample sizes (725 mice) to abide by out IACUC guideles. Our sample sizes are similar to related studies. Yes. Yes. Yes. 5

6 c. Is there any estimate of variance with each group of data? Is the variance similar between groups that are beg statistically compared? Where is this described (section paragraph #)? d. Are tests specified as one or twosided? Two. e. Are there adjustments for multiple comparisons? Yes. TukeyKramer HSD. 3. To promote transparency Nature Neuroscience has stopped allowg bar graphs to report statistics the papers it publishes. If you have bar graphs your paper please make sure to switch them to dotplots (with central and dispersion statistics displayed) or to boxandwhisker plots to show data distributions. 4. Are criteria for excludg data pots reported? Was this criterion established prior to data collection? Where is this described (section paragraph #)? 5. Defe the method of randomization used to assign subjects (or samples) to the experi groups and to collect and process data. If no randomization was used state so. Where does this appear (section paragraph #)? 6. Is a statement of the extent to which vestigator knew the group allocation durg the experiment and assessg outcome cluded? If no bldg was done state so. Where (section paragraph #)? 7. For experiments live vertebrates is a statement of compliance with ethical guideles/regulations cluded? Where (section paragraph #)? 8. Is the species of the animals used reported? Where (section paragraph #)? 9. Is the stra of the animals (cludg background stras of KO/ transgenic animals used) reported? Where (section paragraph #)? SD and SEM were computed and SEM is graphically displayed some figures (it was similar between groups compared). Normality was not explicitly tested. Nonparametric ranksum tests were used to make statistical comparisons. This is described the Methods section and specific tests are described along with the results. Fig 5. and Supp Fig 6 have bar graphs to facilitate comparg mean values. To show the full data distribution for the same data sets we also show complete cumulative histograms. Dark rearg had to be carried out from birth so it was not possible to randomize rearg conditions with a litter. In acute experiments dividual litters contributed pups for multiple time pots. This appears under "Statistical analysis". All the subjects were randomized before data processg/analyses by givg code names by a third person for bldg purposes. From the Methods: "Although it was impossible to completely bld experimenters durg data gatherg (e.g. younger mice are smaller) all subsequent quantification and analysis was performed bld to age and rearg conditions." Yes. Methods first sentence. Yes. Methods second sentence. Yes. Methods second sentence. 10. Is the sex of the animals/subjects used reported? Yes. Methods second sentence. Where (section paragraph #)? 6

7 11. Is the age of the animals/subjects reported? Where (section paragraph #)? 12. For animals housed a vivarium is the light/dark cycle reported? Where (section paragraph #)? 13. For animals housed a vivarium is the housg group (i.e. number of animals per cage) reported? Where (section paragraph #)? 14. For behavioral experiments is the time of day reported (e.g. light or dark cycle)? Where (section paragraph #)? 15. Is the previous history of the animals/subjects (e.g. prior drug admistration surgery behavioral testg) reported? Where (section paragraph #)? a. If multiple behavioral tests were conducted the same group of animals is this reported? Where (section paragraph #)? 16. If any animals/subjects were excluded from analysis is this reported? Where (section paragraph #)? Reagents a. How were the criteria for exclusion defed? Where is this described (section paragraph #)? b. Specify reasons for any discrepancy between the number of animals at the begng and end of the study. Where is this described (section paragraph #)? 1. Have antibodies been validated for use the system under study (assay and species)? a. Is antibody catalog number given? Where does this appear (section paragraph #)? Yes. The ages of the mice used is a key parameter this study and is reported throughout the paper. Yes. Methods second sentence. No. We followed the guideles of our local IACUC and 15 adult mice were house per cage. 7

8 b. Where were the validation data reported (citation supplementary formation Antibodypedia)? Where does this appear (section paragraph #)? 2. Cell le identity a. Are any cell les used this paper listed the database of commonly misidentified cell les mataed by ICLAC and NCBI Biosample? Where (section paragraph #)? b. If yes clude the Methods section a scientific justification of their usedicate here which section and paragraph the justification can be found. c. For each cell le clude the Methods section a statement that specifies: the source of the cell les have the cell les been authenticated? If so by which method? have the cell les been tested for mycoplasma contamation? Where (section paragraph #)? 8

9 Data availability Provide a Data availability statement the Methods section under "Data availability" which should clude where applicable: Accession codes for deposited data Other unique identifiers (such as DOIs and hyperlks for any other datasets) At a mimum a statement confirmg that all relevant data are available from the authors Formal citations of datasets that are assigned DOIs A statement regardg data available the manuscript as source data A statement regardg data available with restrictions See our data availability and data citations policy page for more formation. Data deposition a public repository is mandatory for: a. Prote DNA and RNA sequences b. Macromolecular structures c. Crystallographic data for small molecules d. Microarray data Deposition is strongly recommended for many other datasets for which structured public repositories exist; more details on our data policy are available here. We encourage the provision of other source data supplementary formation or unstructured repositories such as Figshare and Dryad. We encourage publication of Data Descriptors (see Scientific Data) to maximize data reuse. Where is the Data Availability statement provided (section paragraph #)? Computer code/software The data that support the fdgs of this study are available from either correspondg author upon request. Any custom algorithm/software that is central to the methods must be supplied by the authors a usable and readable form for readers at the time of publication. However referees may ask for this formation at any time durg the review process. 1. Identify all custom software or scripts that were required to conduct the study and where the procedures each was used. 2. If computer code was used to generate results that are central to the paper's conclusions clude a statement the Methods section under "Code availability" to dicate whether and how the code can be accessed. Include version formation as necessary and any restrictions on availability. Custom software was used to obta trsic signal optical imagg data. Custom software for trsic signal optical imagg was written by D. Ferster (Northwestern University) and modified the Smith lab. It is available upon request from the correspondg author. The custom code for applyg corrective distortion to the visual stimuli is available onle at: The code for analyzg the 2p imagg data is available upon request. Human subjects 9

10 1. Which IRB approved the protocol? Where is this stated (section paragraph #)? 2. Is demographic formation on all subjects provided? Where (section paragraph #)? 3. Is the number of human subjects their age and sex clearly defed? Where (section paragraph #)? 4. Are the clusion and exclusion criteria (if any) clearly specified? Where (section paragraph #)? 5. How well were the groups matched? Where is this formation described (section paragraph #)? 6. Is a statement cluded confirmg that formed consent was obtaed from all subjects? Where (section paragraph #)? 7. For publication of patient photos is a statement cluded confirmg that consent to publish was obtaed? Where (section paragraph #)? fmri studies For papers reportg functional imagg (fmri) results please ensure that these mimal reportg guideles are met and that all this formation is clearly provided the methods: 1. Were any subjects scanned but then rejected for the analysis after the data was collected? a. If yes is the number rejected and reasons for rejection described? Where (section paragraph #)? 2. Is the number of blocks trials or experi units per session and/ or subjects specified? Where (section paragraph #)? 3. Is the length of each trial and terval between trials specified? 4. Is a blocked eventrelated or mixed design beg used? If applicable please specify the block length or how the eventrelated or mixed design was optimized. 10

11 5. Is the task design clearly described? Where (section paragraph #)? 6. How was behavioral performance measured? 7. Is an ANOVA or factorial design beg used? 8. For data acquisition is a whole bra scan used? If not state area of acquisition. a. How was this region determed? 9. Is the field strength ( Tesla) of the MRI system stated? a. Is the pulse sequence type (gradient/sp echo EPI/spiral) stated? b. Are the fieldofview matrix size slice thickness and TE/TR/ flip angle clearly stated? 10. Are the software and specific parameters (model/functions smoothg kernel size if applicable etc.) used for data processg and preprocessg clearly stated? 11. Is the coordate space for the anatomical/functional imagg data clearly defed as subject/native space or standardized stereotaxic space e.g. origal Talairach MNI305 ICBM152 etc? Where (section paragraph #)? 12. If there was data normalization/standardization to a specific space template are the type of transformation (lear vs. nonlear) used and image types beg transformed clearly described? Where (section paragraph #)? 13. How were anatomical locations determed e.g. via an automated labelg algorithm (AAL) standardized coordate database (Talairach daemon) probabilistic atlases etc.? 14. Were any additional regressors (behavioral covariates motion etc) used? 15. Is the contrast construction clearly defed? 16. Is a mixed/random effects or fixed ference used? a. If fixed effects ference used is this justified? 17. Were repeated measures used (multiple measurements per subject)? 11

12 a. If so are the method to account for with subject correlation and the assumptions made about variance clearly stated? 18. If the threshold used for ference and visualization figures varies is this clearly stated? 19. Are statistical ferences corrected for multiple comparisons? a. If not is this labeled as uncorrected? 20. Are the results based on an ROI (region of terest) analysis? a. If so is the rationale clearly described? b. How were the ROI s defed (functional vs anatomical localization)? 21. Is there correction for multiple comparisons with each voxel? 22. For clusterwise significance is the clusterdefg threshold and the corrected significance level defed? Additional comments Additional Comments 12