Reporting Checklist for Nature Neuroscience

Transcription

1 Correspodig Author: Mauscript Number: Mauscript Type: Galea NNA48318C Article Reportig Checklist for Nature Neurosciece # Figures: 4 # Supplemetary Figures: 2 # Supplemetary Tables: 1 # Supplemetary Videos: 0 This checklist is used to esure good reportig stadards ad to improve the reproducibility of published results. For more iformatio, please read Reportig Life Scieces Research. Please ote that i the evet of publicatio, it is madatory that authors iclude all relevat ological ad statistical iformatio i the mauscript. Statistics reportig, by example example Please specify the followig iformatio for each pael reportig quatitative data, ad where each item is reported (sectio, e.g., & paragraph umber). Each leged should ideally cotai a exact sample size () for each experimetal group/coditio, where is a exact umber ad ot a rage, a clear defiitio of how is defied (for example x cells from x slices from x aimals from x litters, collected over x days), a descriptio of the statistical test used, the results of the tests, ay descriptive statistics ad clearly defied error bars if applicable. For ay experimets usig custom statistics, please idicate the test used ad stats obtaied for each experimet. Each leged should iclude a statemet of how may times the experimet show was replicated i the lab; the details of sample collectio should be sufficietly clear so that the replicability of the experimet is obvious to the reader. For experimets reported i the text but ot i the s, please use the paragraph umber istead of the umber. Note: Mea ad stadard deviatio are ot appropriate o small samples, ad plottig idepedet data poits is usually more iformative. Whe techical replicates are reported, error ad sigificace measures reflect the experimetal variability ad ot the variability of the biological process; it is misleadig ot to state this clearly. FIGURE NUMBER 1a results, TEST USED WHICH TEST? oeway upaired t test Fig. leged EXACT VALUE 9, 9, 10, 15 DEFINED? mice from at least 3 litters/group 15 slices from 10 mice Methods para 8 DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? mea / SEM mea / SEM Fig. leged P VALUE EXACT VALUE p = p = Fig. leged DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE F(3, 36) = 2.97 t(28) = Fig. leged ature eurosciece reportig checklist November 2014 Nature Neurosciece: doi: /

2 FIGURE NUMBER 1D 2B 2B 2C 2C 2D 2E 3B 3B 3B 3C 3C 3C 4B TEST USED WHICH TEST? Repeated measures 1way 1way 1way 1way 1way 1way Idepede t ttest Idepede t ttest Idepede t ttest Idepede t ttest Idepede t ttest Idepede t ttest Idepede t ttest mai mai mai mai mai mai mai EXACT VALUE 12 DEFINED? right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas right haded humas DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM mea / SEM P VALUE EXACT VALUE page 3 DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE F(2,)=4.30 F(2,41)=3.77 F (2,41)=4.05 F(2,41)=5.73 F(2,41)=3. F(2,41)=5.02 F(2,41)=3.77 t(20)=2.16 t(20)=0.59 t(20)=2.58 t(20)=2. t(20)=0.90 t(20)=2.35 t(20)=2.63 page 3 ature eurosciece reportig checklist November 2014 Nature Neurosciece: doi: /

3 4B 4C 4C S2 Idepede t ttest Idepede t ttest Idepede t ttest 1way mai mai mai mai Represetative s right haded humas right haded humas right haded humas right haded humas 1. Are ay represetative images show (icludig Wester blots ad immuohistochemistry/staiig) i the paper? If so, what (s)? 2. For each represetative image, is there a clear statemet of how may times this experimet was successfully repeated ad a discussio of ay limitatios i repeatability? If so, where is this reported (sectio, paragraph #)? Statistics ad geeral s 1. Is there a justificatio of the sample size? If so, how was it justified? Eve if o sample size calculatio 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? a. If there is a sectio summarizig the statistical s i the s, is the statistical test for each experimet clearly defied? b. Do the data meet the assumptios of the specific statistical test you chose (e.g. ormality for a parametric test)? Where is this described (sectio, paragraph #)? mea / SEM mea / SEM mea / SEM mea / SEM No Suppl emet ary Supplem etary t(20)=2.67 t(20)=3. t(20)=2.64 F(2,41)=4.65 Supplem etary No. However, for a huma motor cotrol/learig study group sizes of betwee 1015 people are stadard. This justificatio is provided i the s sectio. Yes. Method: statistical aalysis (page ) Yes Yes. This is ot stated i the mauscript. ature eurosciece reportig checklist November 2014 Nature Neurosciece: doi: /

4 c. Is there ay estimate of variace withi each group of data? Is the variace similar betwee groups that are beig statistically compared? Where is this described (sectio, paragraph #)? d. Are tests specified as oe or twosided? Yes. All 2sided. SEM is provided i all s. There is o specific measure of group variace. e. Are there adjustmets for multiple comparisos? Sigificace level was set at p< Are criteria for excludig data poits reported? Was this criterio established prior to data collectio? Where is this described (sectio, paragraph #)? 4. Defie the of radomizatio used to assig subjects (or samples) to the experimetal groups ad to collect ad process data. If o radomizatio was used, state so. Where does this appear (sectio, paragraph #)? 5. Is a statemet of the extet to which ivestigator kew the group allocatio durig the experimet ad i assessig outcome icluded? If o blidig was doe, state so. 6. For experimets i live vertebrates, is a statemet of compliace with ethical guidelies/regulatios icluded? 7. Is the species of the aimals used reported? 8. Is the strai of the aimals (icludig backgroud strais of KO/ trasgeic aimals used) reported? 9. Is the sex of the aimals/subjects used reported? 10. Is the age of the aimals/subjects reported? 11. For aimals housed i a vivarium, is the light/dark cycle reported? Yes. Method: data aalysis (page 20). Matlab fuctio 'radom' was used to geerate block order i experimet 1, ad participat groups i experimet 2. This is ot stated i the mauscript. No blidig was doe. The motivatioal aspect of this study made this impossible. This is ot stated i the mauscript. Yes. Method: participats (). Yes. Method: participats (). ature eurosciece reportig checklist November 2014 Nature Neurosciece: doi: /

5 12. For aimals housed i a vivarium, is the housig group (i.e. umber of aimals per cage) reported? 13. For behavioral experimets, is the time of day reported (e.g. light or dark cycle)? 14. Is the previous history of the aimals/subjects (e.g. prior drug admiistratio, surgery, behavioral testig) reported? a. If multiple behavioral tests were coducted i the same group of aimals, is this reported? 15. If ay aimals/subjects were excluded from aalysis, is this reported? Reagets a. How were the criteria for exclusio defied? Where is this described (sectio, paragraph #)? b. Specify reasos for ay discrepacy betwee the umber of aimals at the begiig ad ed of the study. Where is this described (sectio, paragraph #)? 1. Have atibodies bee validated for use i the system uder study (assay ad species)? a. Is atibody catalog umber give? Where does this appear (sectio, paragraph #)? b. Where were the validatio data reported (citatio, supplemetary iformatio, Atibodypedia)? Where does this appear (sectio, paragraph #)? 2. If cell lies were used to reflect the properties of a particular tissue or disease state, is their source idetified? No Yes. Method: participats (). ature eurosciece reportig checklist November 2014 Nature Neurosciece: doi: /

6 a. Were they recetly autheticated? Where is this iformatio reported (sectio, paragraph #)? Data depositio Data depositio i a public repository is madatory for: a. Protei, DNA ad RNA sequeces b. Macromolecular structures c. Crystallographic data for small molecules d. Microarray data Depositio is strogly recommeded for may other datasets for which structured public repositories exist; more details o our data policy are available here. We ecourage the provisio of other source data i supplemetary iformatio or i ustructured repositories such as Figshare ad Dryad. We ecourage publicatio of Data Descriptors (see Scietific Data) to maximize data reuse. 1. Are accessio codes for deposit dates provided? Computer code/software Ay custom algorithm/software that is cetral to the s must be supplied by the authors i a usable ad readable form for readers at the time of publicatio. However, referees may ask for this iformatio at ay time durig the review process. 1. Idetify all custom software or scripts that were required to coduct the study ad where i the procedures each was used. 2. If computer code was used to geerate results that are cetral to the paper's coclusios, iclude a statemet i the Methods sectio uder "Code availability" to idicate whether ad how the code ca be accessed. Iclude versio iformatio as ecessary ad ay restrictios o availability. Huma subjects 1. Which IRB approved the protocol? Where is this stated (sectio, paragraph #)? 2. Is demographic iformatio o all subjects provided? 3. Is the umber of huma subjects, their age ad sex clearly defied? No Custom Matlab ad C code was used to collect ad aalyze behavioral data. Methods: experimetal task () ad s: data aalysis (page 20) All computer code used for the collectio ad aalysis of behavioural data is available o request to the correspodig author. This statemet is provided o page 20. Yes. Method: participats (). Yes. Method: participats (). Yes. Method: participats (). ature eurosciece reportig checklist November 2014 Nature Neurosciece: doi: /

7 4. Are the iclusio ad exclusio criteria (if ay) clearly specified? 5. How well were the groups matched? Where is this iformatio described (sectio, paragraph #)? 6. Is a statemet icluded cofirmig that iformed coset was obtaied from all subjects? 7. For publicatio of patiet photos, is a statemet icluded cofirmig that coset to publish was obtaied? fmri studies Yes. Method: participats (). Experimet 1 was a withisubject desig. Experimet 2 was a opportuist sample of youg, healthy huma adults betwee the age rage of 1840 ad so o specific matchig was implemeted. Yes. Method: participats (). For papers reportig fuctioal imagig (fmri) results please esure that these miimal reportig guidelies are met ad that all this iformatio is clearly provided i the s: 1. Were ay subjects scaed but the rejected for the aalysis after the data was collected? a. If yes, is the umber rejected ad reasos for rejectio described? 2. Is the umber of blocks, trials or experimetal uits per sessio ad/ or subjects specified? 3. Is the legth of each trial ad iterval betwee trials specified? 4. Is a blocked, evetrelated, or mixed desig beig used? If applicable, please specify the block legth or how the evetrelated or mixed desig was optimized. 5. Is the task desig clearly described? 6. How was behavioral performace measured? 7. Is a or factorial desig beig used? 8. For data acquisitio, is a whole brai sca used? ature eurosciece reportig checklist November 2014 If ot, state area of acquisitio. Nature Neurosciece: doi: /

8 a. How was this regio determied? 9. Is the field stregth (i Tesla) of the MRI system stated? a. Is the pulse sequece type (gradiet/spi echo, EPI/spiral) stated? b. Are the fieldofview, matrix size, slice thickess, ad TE/TR/ flip agle clearly stated? 10. Are the software ad specific parameters (model/fuctios, smoothig kerel size if applicable, etc.) used for data processig ad preprocessig clearly stated? 11. Is the coordiate space for the aatomical/fuctioal imagig data clearly defied as subject/ative space or stadardized stereotaxic space, e.g., origial Talairach, MNI305, ICBM152, etc? Where (sectio, paragraph #)? 12. If there was data ormalizatio/stadardizatio to a specific space template, are the type of trasformatio (liear vs. oliear) used ad image types beig trasformed clearly described? Where (sectio, paragraph #)? 13. How were aatomical locatios determied, e.g., via a automated labelig algorithm (AAL), stadardized coordiate database (Talairach daemo), probabilistic atlases, etc.? 14. Were ay additioal regressors (behavioral covariates, motio etc) used? 15. Is the cotrast costructio clearly defied? 16. Is a mixed/radom effects or fixed iferece used? a. If fixed effects iferece used, is this justified? 17. Were repeated measures used (multiple measuremets per subject)? a. If so, are the to accout for withi subject correlatio ad the assumptios made about variace clearly stated? 18. If the threshold used for iferece ad visualizatio i s varies, is this clearly stated? 19. Are statistical ifereces corrected for multiple comparisos? ature eurosciece reportig checklist November 2014 a. If ot, is this labeled as ucorrected? Nature Neurosciece: doi: /

9 20. Are the results based o a ROI (regio of iterest) aalysis? a. If so, is the ratioale clearly described? b. How were the ROI s defied (fuctioal vs aatomical localizatio)?. Is there correctio for multiple comparisos withi each voxel?. For clusterwise sigificace, is the clusterdefiig threshold ad the corrected sigificace level defied? Additioal commets Additioal Commets ature eurosciece reportig checklist November 2014 Nature Neurosciece: doi: /