Reporting Checklist for Nature Neuroscience

Transcription

1 Corresponding Author: Manuscript Number: Manuscript Type: Tali Sharot NNA549D Article Reporting Checklist for Nature Neuroscience # Main ures: 4 # lementary ures: 5 # lementary Tables: 4 # lementary Videos: 0 This checklist is used to ensure good reporting standar and to improve the reproducibility of published results. For more information, please read Reporting Life Sciences Research. Please note that in the event of publication, it is mandatory that authors include all relevant methodological and statistical information in the manuscript. Statistics reporting, by figure example example Please specify the following information for each panel reporting quantitative data, and where each item is reported (section, e.g., graph number). Each figure should ideally contain an exact sample size (n) for each experimental group/condition, where n is an exact number and not a range, a clear definition of how n is defined (for example x cells from x slices from x animals from x litters, collected over x days), a description of the statistical used, the results of the s, any descriptive statistics and clearly defined error bars if applicable. For any experiments using custom statistics, please indicate the used and stats obtained for each experiment. Each figure should include a statement of how many times the experiment shown was replicated in 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 in the text but not in the figures, please use the graph number instead of the figure number. Note: Mean and standard deviation are not appropriate on small samples, and plotting independent data points is usually more informative. When technical replicates are reported, error and significance measures reflect the experimental variability and not the variability of the biological process; it is misleading not to state this clearly. FIGURE NUMBER 1a results, TEST USED WHICH TEST? oneway unpaired t SECTION. EXACT VALUE 9, 9, 10, 15 n DEFINED? mice from at least 3 litters/group 15 slices from 10 mice SECTION 8 DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? mean / SEM mean / SEM SECTION. P VALUE EXACT VALUE p = p = SECTION. DEGREES OF FREEDOM F/t/z/R/ETC VALUE VALUE F(3, 3) =.9 t(8) =.808 SECTION. nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 1

2 FIGURE NUMBER 1c 1d 1e ts ts TEST USED WHICH TEST? Pearson correlation Pearson correlation Pearson correlation Steigers z Steigers z SECTION EXACT VALUE n DEFINED? 0 trials 0 trials SECTION DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM SECTION ure ure ure ure ure ure ure 1c ure 1d ure 1e P VALUE EXACT VALUE <0.001 <0.001 p=0.08 p<0.001 p<0.001 SECTION R 1 esults 1 DEGREES OF FREEDOM F/t/z/R/ETC VALUE VALUE F(,49)=4.5 t(5)=3.38 t(5)=. t(5)=0. F(1,51)=8.80 F(1,51)=4.1 r(58)=0. r(58)=0.83 r(58)=0.3 z=4.83 z=.13 SECTION nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44

3 1a 1a 1a 1a ts 3 ts 3 ts 3 ts 3 One Sample T One Sample T One Sample T One Sample T mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM 1a 1a 1a 1a p<0.001 p<0.001 p<0.001 p=0.008 p<0.001 p=0.00 p<0.001 p=0.004 p<0.001 p<0.001 p<0.001 p< F(,5)=4.1 F(1,53)=.44 F(1,53)=39. F(1,53)=. F(,5)=1.11 F(1,53)=.4 F(1,53)=1.99 F(1,53)=8.84 t(54)=43.91 t(54)=4.54 t(54)=158.9 t(54)= nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 3

4 ts 3 ts 3 a c ts ts ts ts c c b One Sample T One Sample T, F, F (Disho nesty Escalat ion ) (Disho nesty Escalat ion ) (Disho nesty Escalat ion ) (Disho nesty Escalat ion ) (Disho nesty Escalat ion ) (Disho nesty Escalat ion ) (Disho nesty Magnit ude ) p<0.001 p<0.001 mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM a c c c c c c c b p=0.8 p=0.01 p=0.01 p=0.01 p=0.40 p=0.58 p=0.8 p=0. p=0.0 t(54)=1.3 t(54)=10.34 F(1,4)=1.4 F(1,0)=. t(3)=. t(3)=. t(3)=0.85 t(3)=0.5 F(1,0)=0.08 F(1,0)=0. F(1,0)=3.50 nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 4

5 ts ts ts ts ts ts ts ts ts ts ts 3b 3b 3b a t t paired sample t t fmri fmri fmri fmri p=0.01 p=0.9 p=0.31 p=0.9 p=0.4 p=0.10 p=0.5 p=0.54 p=0.3 p=0.11 p=0.3 mean / SEM mean / SEM mean / SEM mean / SEM 3b 3b 3b a p=0.0 p=0.0 p=0.00 p= F(1,1)=5.4 t(53)=0.41 t(53)=1.0 t(53)=1.0 t(3)=0. t(3)=1.1 t(53)=0.5 t(53)=0.1 t(53)=0.91 t(3)=1.8 t(3)=0.93 t(4)=.3 t(4)=1.93 t(4)=.9 t(4)= nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 5

6 a a ts 10 ts 10 ts 10 4c 4c 4c b b b Met ho t paired sample t t t paired sample t t t paired sample t t t paired sample t / fmri fmri fmri fmri fmri fmri fmri fmri fmri fmri fmri fmri/ non fmri mean / SEM mean / SEM a a p=0.38 p=0.0 p=0.94 p=0.0 p=0.40 mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM 4c 4c 4c b b b p=0.01 p=0.14 p=0.01 p=0.03 p=0.09 p=0.01 p= t(4)=0.9 t(4)=.0 t(4)=0.08 t(4)=1.31 t(4)=0.85 t(4)=.48 t(4)=1.53 t(4)=.8 t(4)=.30 t(4)=1. t(4)=3.05 t(53)= nature neuroscience reporting checklist March 01 Met ho 30/ fmri/ non fmri p=0.93 t(53)=0.10 Nature Neuroscience: doi: /nn.44

7 Met ho Met ho Met ho Met ho a a b b c c 3 3 4a 4b t vs 0 t vs 0 t vs 0 t vs 0 t vs 0 t vs 0 t vs 0 t vs / 30/ 30/ 30/ fmri/ non fmri fmri/ non fmri fmri/ non fmri fmri/ non fmri asked awareness q asked awareness q 1 3 p. 3 p. 4 4 p=0.48 p=0. p=0.5 p=0.1 mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM mean / SEM a a b b c c p=0. p=0.01 p=0.3 p=0.04 p=0.001 p<0.001 p=0.1 p>0.95 p=0. p<0.001 p= t(53)=0.1 t(53)=1.11 t(53)=0.58 t(53)=1.40 F(1,51)=0.18 t(4)=3.11 t(4)=0.9 t(4)=.11 t(4)=3.8 t(3)=4.53 t(3)=1. t(14)=0.04 t(14)=1.9 t(54)=19.0 t(54)= nature neuroscience reporting checklist March 01 5 Paired sample t 5 5 mean / SEM 5 p= t(54)=.19 5 Nature Neuroscience: doi: /nn.44

8 Tabl e Tabl e One Sample ts vs 0 Paired Sample ts Table Table Representative figures fmri fmri Table Table 1. Are any representative images shown (including Western blots and immunohistochemistry/staining) in the paper? If so, what figure(s)?. For each representative image, is there a clear statement of how many times this experiment was successfully repeated and a discussion of any limitations in repeatability? If so, where is this reported (section, graph #)? Statistics and general metho 1. Is there a justification of the sample size? If so, how was it justified? Even if no sample size calculation was performed, authors should report why the sample size is adequate to measure their effect size.. Are statistical s justified as appropriate for every figure? a. If there is a section summarizing the statistical metho in the metho, is the statistical for each experiment clearly defined? b. Do the data meet the assumptions of the specific statistical you chose (e.g. normality for a metric )? Where is this described (section, graph #)? NA: p=0.18; p=0.9; p=0.9; p=0.58; DPLFC: p=0.4; p=0.03; p=0.3; p=0.35; AI: p=0.1; p=0.; p=0.05; p=0.88 NA: p=0.4; p=0.3; DLPFC: p=0.04; p=0.11; AI: p=0.10; p=0.0 Table Table Yes. Example scatter plot, figure 4b. NA: t(4)=1.3; t(4)=0.10; t(4)=0.11; t(4)=0.5; DLPFC:t(4)=0.3 ; t(4)=.3; t(4)=1.; t(4)=0.9 AI: t(4)=1.4; t(4)=1.1; t(4)=.11; t(4)=0.1 NA: t(4)=0.48; t(4)=0.49; DLPFC:t(4)=.18 ; t(4)=1.4; AI: t(4)=1.1; t=1.9 All subjects are used in the analysis to determine if there are significant effects at the group level. Table Table Sample size based on pilot study. This is stated in the Statistics section at the end of the online. We followed standard procedures in the field. Yes. Data distribution was assumed to be normal, but not formally ed. This is stated in the statistics section at the end of the online. nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 8

9 c. Is there any estimate of variance within each group of data? Is the variance similar between groups that are being statistically compared? Where is this described (section, graph #)? Yes. Means and standard errors are shown on each figure and described in figure s. Between group variance irrelevant here (within subject design). d. Are s specified as one or twosided? Twosided (ts), Onesided (F s). This is stated in the statistics section at the end of the online. e. Are there adjustments for multiple comparisons? No, none needed. 3. To promote transparency, Nature Neuroscience has stopped allowing bar graphs to report statistics in the papers it publishes. If you have bar graphs in 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 excluding data points reported? Was this criterion established prior to data collection? Where is this described (section, graph #)? 5. Define the method of randomization used to assign subjects (or samples) to the experimental groups and to collect and process data. If no randomization was used, state so. Where does this appear (section, graph #)?. Is a statement of the extent to which investigator knew the group allocation during the experiment and in assessing outcome included? If no blinding was done, state so.. For experiments in live vertebrates, is a statement of compliance with ethical guidelines/regulations included? 8. Is the species of the animals used reported? 9. Is the strain of the animals (including background strains of KO/ transgenic animals used) reported? Barplots include datapoints No data points were excluded. No randomization was used as all subjects complete all conditions (i.e. within subject design). Counterbalancing was used to control for different orderings of conditions (stated in ). No groups (within subject design) therefore blinding not required. nature neuroscience reporting checklist March Is the sex of the animals/subjects used reported? Nature Neuroscience: doi: /nn.44 9

10 11. Is the age of the animals/subjects reported? 1. For animals housed in a vivarium, is the light/dark cycle reported? 13. For animals housed in a vivarium, is the housing group (i.e. number of animals per cage) reported? 14. For behavioral experiments, is the time of day reported (e.g. light or dark cycle)? 15. Is the previous history of the animals/subjects (e.g. prior drug administration, surgery, behavioral ing) reported? a. If multiple behavioral s were conducted in the same group of animals, is this reported? 1. If any animals/subjects were excluded from analysis, is this reported? Reagents a. How were the criteria for exclusion defined? Where is this described (section, graph #)? b. Specify reasons for any discrepancy between the number of animals at the beginning and end of the study. Where is this described (section, graph #)? 1. Have antibodies been validated for use in the system under study (assay and species)? a. Is antibody catalog number given? Where does this appear (section, graph #)? Yes, first graph for and section of headed Participants (Experiment ) for No. nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 10

11 b. Where were the validation data reported (citation, supplementary information, Antibodypedia)? Where does this appear (section, graph #)?. Cell line identity a. Are any cell lines used in this paper listed in the database of commonly misidentified cell lines maintained by ICLAC and NCBI Biosample? b. If yes, include in the section a scientific justification of their useindicate here in which section and graph the justification can be found. c. For each cell line, include in the section a statement that specifies: the source of the cell lines have the cell lines been authenticated? If so, by which method? have the cell lines been ed for mycoplasma contamination? nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 11

12 Data availability Provide a Data availability statement in the section under "Data availability", which should include, where applicable: Accession codes for deposited data Other unique identifiers (such as DOIs and hyperlinks for any other datasets) At a minimum, a statement confirming that all relevant data are available from the authors Formal citations of datasets that are assigned DOIs A statement regarding data available in the manuscript as source data A statement regarding data available with restrictions See our data availability and data citations policy page for more information. Data deposition in a public repository is mandatory for: a. Protein, 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 in supplementary information or in unstructured repositories such as share and Dryad. We encourage publication of Data Descriptors (see Scientific Data) to maximize data reuse. Where is the Data Availability statement provided (section, graph #)? Computer code/software We include a Data Availability statement ad the end of the online section. Any custom algorithm/software that is central to the metho must be supplied by the authors in a usable and readable form for readers at the time of publication. However, referees may ask for this information at any time during the review process. 1. Identify all custom software or scripts that were required to conduct the study and where in the procedures each was used.. If computer code was used to generate results that are central to the paper's conclusions, include a statement in the section under "Code availability" to indicate whether and how the code can be accessed. Include version information as necessary and any restrictions on availability. Custom MATLAB scripts were used for parts of the fmri analysis. MATLAB scripts are available on request. This is stated at the end of the online section (under "Code Availability"). nature neuroscience reporting checklist March 01 Human subjects Nature Neuroscience: doi: /nn.44 1

13 1. Which IRB approved the protocol? Where is this stated (section, graph #)?. Is demographic information on all subjects provided? 3. Is the number of human subjects, their age and sex clearly defined? 4. Are the inclusion and exclusion criteria (if any) clearly specified? 5. How well were the groups matched? Where is this information described (section, graph #)?. Is a statement included confirming that informed consent was obtained from all subjects?. For publication of patient photos, is a statement included confirming that consent to publish was obtained? fmri studies UCL Psychology Ethics Committee. Stated in, graph 1. (graph 1). (graph 1). (graph 1). all complete all conditions (i.e. within subject design) (graph 1). No photos are included. For papers reporting functional imaging (fmri) results please ensure that these minimal reporting guidelines are met and that all this information is clearly provided in the metho: 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?. Is the number of blocks, trials or experimental units per session and/ or subjects specified? Yes (n=3). Yes. (graph 1). Yes, 0 trials per block. 4 blocks in total. graph. 3. Is the length of each trial and interval between trials specified? graph 5 and 1a. nature neuroscience reporting checklist March Is a blocked, eventrelated, or mixed design being used? If applicable, please specify the block length or how the eventrelated or mixed design was optimized. Eventrelated. Nature Neuroscience: doi: /nn.44 13

14 5. Is the task design clearly described? Yes. (Procedure and Paradigm section).. How was behavioral performance measured? Quantified dishonesty by comparing responses (advice) to stimuli in different conditions compared to a baseline condition. This is outlined in (Behavioral Analysis section).. Is an or factorial design being used? ANCOVA 8. For data acquisition, is a whole brain scan used? If not, state area of acquisition. 40 slices per volume were collected for each participant. This means that for some we are missing coverage for the superior parietal lobe which was not relevant for our investigation. a. How was this region determined? Protocol used by us in past studies. 9. Is the field strength (in Tesla) of the MRI system stated? Yes (1.5 Tesla), stated in (Image Acquisition section) a. Is the pulse sequence type (gradient/spin 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 meters (/functions, smoothing kernel size if applicable, etc.) used for data processing and preprocessing clearly stated? 11. Is the coordinate space for the anatomical/functional imaging data clearly defined as subject/native space or standardized stereotaxic space, e.g., original Talairach, MNI305, ICBM15, etc? Where (section, graph #)? 1. If there was data normalization/standardization to a specific space template, are the type of transformation (linear vs. nonlinear) used and image types being transformed clearly described? Where (section, graph #)? 13. How were anatomical locations determined, e.g., via an automated labeling algorithm (AAL), standardized coordinate database (Talairach daemon), probabilistic atlases, etc.? 14. Were any additional regressors (behavioral covariates, motion etc) used? Yes, (Image Acquisition Section). Yes, (Image Acquisition Section). Yes, (Image Acquisition Section). Standardized stereotaxic space (MNI space). Stated in (Image Acquisition Section). th degree Bspline transformation applied. This is stated in (Image Acquisition Section). ROI anatomically defined by generating a statistical reverse inference map in Neurosynth for the term emotion. This is stated in results (graph 10) and online (fmri Analysis section, ROI, sub section). The ROI is displayed in ure 3a. Yes, motion correction regressors from realignment procedure were included in both analysis. This is stated in (Time Weighted Dishonesty section and Prediction Analysis sections). 15. Is the contrast construction clearly defined? Yes. (Time Weighted Dishonesty section) nature neuroscience reporting checklist March Is a mixed/random effects or fixed inference used? Mixed/Random effects a. If fixed effects inference used, is this justified? Nature Neuroscience: doi: /nn.44 14

15 1. Were repeated measures used (multiple measurements per subject)? Yes (one measure per subject per condition). a. If so, are the method to account for within subject correlation and the assumptions made about variance clearly stated? 18. If the threshold used for inference and visualization in figures varies, is this clearly stated? 19. Are statistical inferences corrected for multiple comparisons? No a. If not, is this labeled as uncorrected? 0. Are the results based on an ROI (region of interest) analysis? Yes. a. If so, is the rationale clearly described? Yes. b. How were the ROI s defined (functional vs anatomical localization)? 1. Is there correction for multiple comparisons within each voxel?. For clusterwise significance, is the clusterdefining threshold and the corrected significance level defined? Additional comments Additional Comments Yes. Paired ts used to compare repeat measurements. ROI anatomically defined by generating a statistical reverse inference map in Neurosynth for the term emotion. This is stated in results (graph 10) and online (fmri analysis, ROI). The ROI is displayed in ure 3a. None. nature neuroscience reporting checklist March 01 Nature Neuroscience: doi: /nn.44 15