Reporting Checklist for Nature Neuroscience
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1 Coesponding Autho: Manuscipt Numbe: Manuscipt Type: Yuki Oka NNA5991A Aticle Repoting Checklist fo Natue Neuoscience # Main Figues: 7 # Supplementay Figues: # Supplementay Tables: 0 # Supplementay Videos: 2 This checklist is used to ensue good epoting standads and to impove the epoducibility of published esults. Fo moe infomation, please ead Repoting Life Sciences Reseach. Please e that in the event of publication, it is mandatoy that authos include all elevant methodological and statistical infomation in the manuscipt. Statistics epoting, by figue example example Please specify the following infomation fo each panel epoting quantitative data, and whee each item is (section, e.g., & paagaph numbe). Each figue should ideally contain an exact sample size (n) fo each expeimental goup/condition, whee n is an exact numbe and a ange, a clea definition of how n is defined (fo example x cells fom x slices fom x animals fom x littes, collected ove x days), a desciption of the statistical test used, the esults of the tests, any desciptive statistics and clealy defined eo bas if applicable. Fo any expeiments using custom statistics, please indicate the test used and stats obtained fo each expeiment. Each figue should include a statement of how many times the expeiment shown was eplicated in the lab; the details of sample collection should be sufficiently clea so that the eplicability of the expeiment is obvious to the eade. Fo expeiments in the text but in the figues, please use the paagaph numbe instead of the figue numbe. Note: Mean and standad deviation ae appopiate on small samples, and plotting independent data points is usually moe infomative. When technical eplicates ae, eo and significance measues eflect the expeimental vaiability and the vaiability of the biological pocess; it is misleading to state this clealy. FIGURE NUMBER 1a esults, paa TEST USED WHICH TEST? oneway ANOVA unpaied t test Fig. paa EXACT VALUE 9, 9, 10, 15 n DEFINED? 3 littes/goup 15 slices fom 10 mice Methods paa 8 paa DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? Fig. paa P VALUE EXACT VALUE p = 0.0 p = Fig. paa DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE F(3, 3) = 2.97 t(28) = Fig. paa 1
2 FIGURE NUMBER 1a: H20 saliva 1b: bic minu s bic 1d 2b: ami 2c: 7a:n eve 20m M cont ol doub le 7b: nev e 8m W doub le cont ol 3a: ph b:w ate 3c:d oz befo e afte TEST USED WHICH TEST? 2tailed paied t test 2 tailed paied t test EXACT VALUE 7, 3, 5,3 9 n DEFINED? DESCRIPTIVE STATS (AVERAGE, VARIANCE) REPORTED? P VALUE EXACT VALUE p=0.000 p=0.028 p=0.028 p=0.2 p= p= p=0.028 p= p= p= DEGREES OF FREEDOM & F/t/z/R/ETC VALUE VALUE U=3 t=3.509 t=5.3 2
3 3C:b benz befo e afte ex.fig.3a:c ahe t hom e ex.fig.3d:i se time c e: total light total e: 310 min light 5b c e Ex b: cont ol at 5min oil Ex c: TeNT 5 tials Ex c cont ol 13 tials 2 tailed paied t test twotailed twotailed twotailed twotailed twotailed twotailed Mann Whitney U twotailed twotailed twotailed 8, mice fom the same litte mice fom the same litte 3 mice fom 7 fo PKD2L1T ent and fo contol 3 p= p=0.0 p= p= p=0.015 p= p=0.02 p< P= t=3.58 U=15 t=3.337 t=8.22 t=.73 t=.082 t=11.52 t=.8 t=.3 t=
4 Ex c: cont ol All twotailed Repesentative figues 1. Ae any epesentative images shown (including Westen blots and immunohistochemisty/staining) in the pape? If so, what figue(s)? 2. Fo each epesentative image, is thee a clea statement of how many times this expeiment was successfully epeated and a discussion of any limitations in epeatability? If so, whee is this (section, paagaph #)? Statistics and geneal methods 1. Is thee a justification of the sample size? If so, how was it justified? Even if no sample size calculation was pefomed, authos should epot why the sample size is adequate to measue thei effect size. 2. Ae statistical tests justified as appopiate fo evey figue? a. If thee is a section summaizing the statistical methods in the methods, is the statistical test fo each expeiment clealy defined? b. Do the data meet the assumptions of the specific statistical test you chose (e.g. nomality fo a paametic test)? Whee is this descibed (section, paagaph #)? c. Is thee any estimate of vaiance within each goup of data? Is the vaiance simila between goups that ae being statistically compaed? Whee is this descibed (section, paagaph #)? Figue 5 and Supplemental Figue 5 Mateials and Methods, Histology section t=1.29 Sample sizes wee chosen based on pio liteatue in the field. This is mentioned in Methods section. Statistical tests wee chosen based on the natue of the data Each test used was defined in the figue s d. Ae tests specified as one o twosided? Specified in Figue s As is common in pio liteatue, the test was used so as to assume a nomal distibution of the data. the standad eo of the mean is in each figue. Vaiance is simila between diffeent goups being compaed e. Ae thee adjustments fo multiple compaisons? No
5 3. To pomote tanspaency, Natue Neuoscience has stopped allowing ba gaphs to epot statistics in the papes it publishes. If you have ba gaphs in you pape, please make sue to switch them to dotplots (with cental and dispesion statistics displayed) o to boxandwhiske plots to show data distibutions.. Ae citeia fo excluding data points? Was this citeion established pio to data collection? Whee is this descibed (section, paagaph #)? 5. Define the method of andomization used to assign subjects (o samples) to the expeimental goups and to collect and pocess data. If no andomization was used, state so. Whee does this appea (section, paagaph #)?. Is a statement of the extent to which investigato knew the goup allocation duing the expeiment and in assessing outcome included? If no blinding was done, state so. 7. Fo expeiments in live vetebates, is a statement of compliance with ethical guidelines/egulations included? 8. Is the species of the animals used? 9. Is the stain of the animals (including backgound stains of KO/ tansgenic animals used)? 10. Is the sex of the animals/subjects used? 11. Is the age of the animals/subjects? 12. Fo animals housed in a vivaium, is the light/dak cycle? All ba gaphs wee switched to dotplots. Methods, Statistical analysis No andomization was used fo the data collection. No blinding was done fo data used fo the pape. Howeve, key behavioal expeiments such as lightdiven dinking wee epeated by othe lab membes in a blind fashion. 13. Fo animals housed in a vivaium, is the housing goup (i.e. numbe of animals pe cage)? 5
6 1. Fo behavioal expeiments, is the time of day (e.g. light o dak cycle)? 15. Is the pevious histoy of the animals/subjects (e.g. pio dug administation, sugey, behavioal testing)? a. If multiple behavioal tests wee conducted in the same goup of animals, is this? 1. If any animals/subjects wee excluded fom analysis, is this? Reagents a. How wee the citeia fo exclusion defined? Whee is this descibed (section, paagaph #)? b. Specify easons fo any discepancy between the numbe of animals at the beginning and end of the study. Whee is this descibed (section, paagaph #)? 1. Have antibodies been validated fo use in the system unde study (assay and species)? a. Is antibody catalog numbe given? Whee does this appea (section, paagaph #)? b. Whee wee the validation data (citation, supplementay infomation, Antibodypedia)? Whee does this appea (section, paagaph #)? 2. Cell line identity a. Ae any cell lines used in this pape listed in the database of commonly misidentified cell lines maintained by ICLAC and NCBI Biosample? Methods, Statistics section Data points wee excluded fom the analysis if sugey was unsuccessful. Methods, Histology section Methods, Histology section Methods, Histology section b. If yes, include in the Methods section a scientific justification of thei useindicate hee in which section and paagaph the justification can be found.
7 c. Fo each cell line, include in the Methods section a statement that specifies: the souce of the cell lines have the cell lines been authenticated? If so, by which method? have the cell lines been tested fo mycoplasma contamination? Data availability Povide a Data availability statement in the Methods section unde "Data availability", which should include, whee applicable: Accession codes fo deposited data Othe unique identifies (such as DOIs and hypelinks fo any othe datasets) At a minimum, a statement confiming that all elevant data ae available fom the authos Fomal citations of datasets that ae assigned DOIs A statement egading data available in the manuscipt as souce data A statement egading data available with estictions See ou data availability and data citations policy page fo moe infomation. Data deposition in a public epositoy is mandatoy fo: a. Potein, DNA and RNA sequences b. Macomolecula stuctues c. Cystallogaphic data fo small molecules d. Micoaay data Deposition is stongly ecommended fo many othe datasets fo which stuctued public epositoies exist; moe details on ou data policy ae available hee. We encouage the povision of othe souce data in supplementay infomation o in unstuctued epositoies such as Figshae and Dyad. We encouage publication of Data Desciptos (see Scientific Data) to maximize data euse. Whee is the Data Availability statement povided (section, paagaph #)? Compute code/softwae Methods, Data availability section; the souce data was povided Any custom algoithm/softwae that is cental to the methods must be supplied by the authos in a usable and eadable fom fo eades at the time of publication. Howeve, efeees may ask fo this infomation at any time duing the eview pocess. 1. Identify all custom softwae o scipts that wee equied to conduct the study and whee in the pocedues each was used. 7
8 2. If compute code was used to geneate esults that ae cental to the pape's conclusions, include a statement in the Methods section unde "Code availability" to indicate whethe and how the code can be accessed. Include vesion infomation as necessay and any estictions on availability. Human subjects 1. Which IRB appoved the potocol? Whee is this stated (section, paagaph #)? 2. Is demogaphic infomation on all subjects povided? 3. Is the numbe of human subjects, thei age and sex clealy defined?. Ae the inclusion and exclusion citeia (if any) clealy specified? 5. How well wee the goups matched? Whee is this infomation descibed (section, paagaph #)?. Is a statement included confiming that infomed consent was obtained fom all subjects? 7. Fo publication of patient photos, is a statement included confiming that consent to publish was obtained? Additional comments Additional Comments 8
Reporting Checklist for Nature Neuroscience
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