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eLife Sciences Publications, Ltd is a limited liability non-profit non-stock corporation incorporated in the State of
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eLife’s!transparent!reporting!form!
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We"encourage"authors"to"provide"detailed"information"within&their&submission"to"facilitate"
the"interpretation"and"replication"of"experiments."Authors"can"upload"supporting"
documentation"to"indicate"the"use"of"appropriate"reporting"guidelines"for"health-related"
research"(see"EQUATOR"Network),"life"science"research"(see"the"BioSharing"Information"
Resource),"or"the"ARRIVE"guidelines"for"reporting"work"involving"animal"research."Where"
applicable,"authors"should"refer"to"any"relevant"reporting"standards"documents"in"this"form."
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If"you"have"any"questions,"please"consult"our"Journal"Policies"and/or"contact"us:"
editorial@elifesciences.org.!
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Sample-size!estimation"
You"should"state"whether"an"appropriate"sample"size"was"computed"when"the"
study"was"being"designed""
You"should"state"the"statistical"method"of"sample"size"computation"and"any"
required"assumptions"
If"no"explicit"power"analysis"was"used,"you"should"describe"how"you"decided"what"
sample"(replicate)"size"(number)"to"use"
"
Please"outline"where"this"information"can"be"found"within"the"submission"(e.g.,"sections"or"
figure"legends),"or"explain"why"this"information"doesn’t"apply"to"your"submission:"
"
Replicates"
You"should"report"how"often"each"experiment"was"performed"
You"should"include"a"definition"of"biological"versus"technical"replication"
The"data"obtained"should"be"provided"and"sufficient"information"should"be"
provided"to"indicate"the"number"of"independent"biological"and/or"technical"
replicates"
If"you"encountered"any"outliers,"you"should"describe"how"these"were"handled"
Criteria"for"exclusion/inclusion"of"data"should"be"clearly"stated"
High-throughput"sequence"data"should"be"uploaded"before"submission,"with"a"
private"link"for"reviewers"provided"(these"are"available"from"both"GEO"and"
ArrayExpress)"
"
Please"outline"where"this"information"can"be"found"within"the"submission"(e.g.,"sections"or"
figure"legends),"or"explain"why"this"information"doesn’t"apply"to"your"submission:"
!
! !
"
"
With one exception our data are based on results from 3 independently analyzed animals. This number of animals provided statistically significant results.
Our statistical methods of comparing sequences from mice of different genotypes involved Jaccard or Anne Chao Jaccard methods, mentioned and
referenced in the results section. We used DeSeq2 to compare use of TRAVs and TRAJs between mice of different genotypes as described in Materials and
Methods and the legends to Supplementary Figures 5 and 7. Student t tests or one way ANOVA with Newman-Keuls or Bonferroni post test corrections was
used to compare some results between mice of different genotypes as described in the Legends to Figures 1, 2, 4, 5, 7, 8 and supplementary Figures 2, 8
and 9.
The number of times experiments were done are reported in each Figure Legend. These are
all biological replicates, that is, experiments were done with individual mice on different days.
No outliers were reported.
Our sequences, before and after analysis are deposited at GEO accession GSE105129.
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eLife Sciences Publications, Ltd is a limited liability non-profit non-stock corporation incorporated in the State of
Delaware, USA, with company number 5030732, and is registered in the UK with company number FC030576 and
branch number BR015634 at the address 1st Floor, 24 Hills Road, Cambridge CB2 1JP | August 2014
2!
Statistical!reporting"
Statistical"analysis"methods"should"be"described"and"justified"
Raw"data"should"be"presented"in"figures"whenever"informative"to"do"so"(typically"
when"N"per"group"is"less"than"10)"
For"each"experiment,"you"should"identify"the"statistical"tests"used,"exact"values"of"
N,"definitions"of"center,"methods"of"multiple"test"correction,"and"dispersion"and"
precision"measures"(e.g.,"mean,"median,"SD,"SEM,"confidence"intervals;"and,"for"the"
major"substantive"results,"a"measure"of"effect"size"(e.g.,"Pearson's"r,"Cohen's"d)"
Report"exact"p-values"wherever"possible"alongside"the"summary"statistics"and"95%"
confidence"intervals."These"should"be"reported"for"all"key"questions"and"not"only"
when"the"p-value"is"less"than"0.05."
"
Please"outline"where"this"information"can"be"found"within"the"submission"(e.g.,"sections"or"
figure"legends),"or"explain"why"this"information"doesn’t"apply"to"your"submission:"
"
(For"large"datasets,"or"papers"with"a"very"large"number"of"statistical"tests,"you"may"upload"a"
single"table"file"with"tests,"Ns,"etc.,"with"reference"to"sections"in"the"manuscript.)!
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Group!allocation!
Indicate"how"samples"were"allocated"into"experimental"groups"(in"the"case"of"
clinical"studies,"please"specify"allocation"to"treatment"method);"if"randomization"
was"used,"please"also"state"if"restricted"randomization"was"applied"
Indicate"if"masking"was"used"during"group"allocation,"data"collection"and/or"data"
analysis!
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Please"outline"where"this"information"can"be"found"within"the"submission"(e.g.,"sections"or"
figure"legends),"or"explain"why"this"information"doesn’t"apply"to"your"submission:"
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Additional!data!files!(“source!data”)!
We"encourage"you"to"upload"relevant"additional"data"files,"such"as"numerical"data"
that"are"represented"as"a"graph"in"a"figure,"or"as"a"summary"table"
Where"provided,"these"should"be"in"the"most"useful"format,"and"they"can"be"
uploaded"as"“Source"data”"files"linked"to"a"main"figure"or"table"
Include"model"definition"files"including"the"full"list"of"parameters"used"
Include"code"used"for"data"analysis"(e.g.,"R,"MatLab)"
Avoid"stating"that"data"files"are"“available"upon"request”"
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Please"indicate"the"figures"or"tables"for"which"source"data"files"have"been"provided:"
"
"
"
"
Our statistical methods of comparing sequences from mice of different genotypes involved Jaccard or Anne Chao Jaccard methods,
mentioned and referenced in the results section. We used DeSeq2 to compare use of TRAVs and TRAJs between mice of different
genotypes as described in Materials and Methods and the legends to Supplementary Figures 5 and 7. Student t tests or one way
ANOVA with Newman-Keuls or Bonferroni post test corrections was used to compare some results between mice of different
genotypes as described in the Legends to Figures 1, 2, 4, 5, 7, 8 and supplementary Figures 2, 8 and 9.
In these experiments all groups were experimental since we were
comparing results between genetically different mice
Figure 1
Figure 2
For all other Figures Source data are at GEO GSE105129
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