of 4
1
M
aterials
D
esign
A
nalysis
R
eporting (MDAR)
Checklist
for Authors
The
MDAR
framework establishes
a
minimum se
t of requirements in transparent reporting applicable to studies in the life sciences
(
see Statement of Task:
doi:10.31222/osf.io/9sm4x.
)
.
The MDAR checklist is a tool for authors, editors and others seeking to
adopt
the MDAR framework for transparent reporting in manuscripts and other outputs. Please refer to the
MDAR Elaboration
Document
for
additional
context for the MDAR framework.
2
Materials
Antibodies
Yes (indicate where provided
:
page
no/section/legend
)
n/a
For commercial reagents,
provide
supplier
name, catalog
ue
number and RRID
,
if available.
n/a
Cell materials
Yes (indicate where provided
:
page
no/section/legend
)
n/a
Cell lines:
P
rovide
species
information, strain.
Provide
accession number in repository
OR
supplier name, catalog number, clone number,
OR
RRID
n/a
Primary cultures:
P
rovide
species, strain, sex of
origin, genetic
modification status
.
n/a
Experimental animals
Yes (indicate where provided
:
page
no/section/legend
)
n/a
Laboratory animals:
P
rovide s
pecies, strain, sex, age,
genetic modification status
.
Provide
a
ccession
number in repository
OR
supplier name, catalog
number, clone number,
OR
RRID
n/a
Animal observed in or captured from the
field
:
Provide s
pecies, sex and age where
possible
n/a
Model organisms:
Provide
Accession number
in repository (where relevant)
OR
RRID
n/a
Plants and microbes
Yes (indicate where provided: page no/section/legend)
n/a
Plants:
provide species and strain, unique accession
number if available, and source (including locat
ion
for collected wild specimens
)
n/a
Microbes:
provide species and strain
, unique
accession
number if available, and source
Materials and Methods,
Pseudomonas aeruginosa
strain
UCBPP
-
PA14
.
Human research participants
Yes (indicate where
provided
:
page
no/section/legend
)
n/a
Identify authority granting ethics approval
(IRB
or
equivalent committee(s)
, provide reference number
for approval
.
n/a
Provide statement confirming informed consent
obtained from study participants.
n/a
Report on a
ge and sex
for all study participants.
n/a
3
Design
Study
protocol
Yes (indicate where provided
:
page
no/section/legend
)
n/a
For clinical trials, provide the
trial registration
number
OR
cite
DOI
in manuscript.
n/a
Laboratory
protocol
Yes (indicate where provided
:
page
no/section/legend
)
n/a
Provide DOI or other citation details if
detailed step
-
by
-
step
protocols are available.
n/a
Experimental study design (statistics details)
Yes (indicate where
provided
:
page
no/section/legend
)
n/a
S
tate whether and
how the following have been
done
, or
if they were
not carried out
.
Sample size determination
n/a
Randomisation
n/a
Blinding
n/a
Inclusion/exclusion criteria
n/a
Sample
definition and in
-
laboratory replication
Yes (indicate where provided
:
page
no/section/legend
)
n/a
State number of times the experiment was
replicated in laboratory
One replicate for the LB and SCFM growth curves. One
replicate for the 10h and 35h
biofilm experiments.
Define whether data describe technical or biological
replicates
Different experiments, each performed once.
Ethics
Yes (indicate where provided
: pa
ge
no/section/legend
)
n/a
Studies involving human participants:
State details of
authority granting ethics approval (IRB
or equivalent
committee(s), provide reference number for
approval.
n/a
Studies involving experimental animals:
State details
of authority granting ethics approval (IRB
or
equivalent committee(s), provide reference number
for approval.
n/a
Studies involving specimen and field samples: State if
relevant permits obtained, provide details of
authority approving study
; if none were required,
explain why.
n/a
Dual Use Research of Concern (DURC)
Yes (indicate where provided
:
page
no/section/legend
)
n/a
If
study is
subject to dual use research of
concern,
state
the authority granting approval and
reference
number for the regulatory approval
n/a
4
Analysis
Attrition
Yes (indicate where provided
:
page
no/section/legend
)
n/a
State if
sample or data point from the analysis
is
excluded,
and
whether the criteria for exclusion were
determined and specified in advance.
Materials and Methods: Single
-
cell UMAP analysis was performed using Scanpy
v1.7.0 (99). Genes detected at consistently low levels were excluded from the
analysis. These included
pilY1, flgK, nasA, algU, purF, phzH, phzS and pslG (table S1).
Statistics
Yes (indicate where provided
:
page
no/section/legend
)
n/a
Describe
statistical tests used and justify choice of
tests.
Materials and Methods
, scanpy analysis:
w
e used
the standard
Wilcoxon
rank
-
sum
test with Benjamini
-
Hochberg correction for
determination of enriched genes.
Data Availability
Yes (indicate where provided
:
page
no/section/legend
)
n/a
State
whether newly created da
tasets are
available,
including protocols
for access or restriction on
access.
Source data is available on Zenodo.
If data are publicly available,
provide
accessi
on
number in repository or DOI
or
URL.
http://doi.org/ 10.5281/zenodo.4767568
If
publicly available data are reused,
provide
accession number in repository or DOI or URL, where
possible.
Code Availability
Yes (indicate where provided
:
page
no/section/legend
)
n/a
F
or all newly generated code and software essential
for
replicating the main findings of the study:
State
whether the code or software is available.
The code is available at
Z
enodo
If code is publicly available,
provide
accessi
on
number in repository, or DOI or URL.
http://doi.org/
10.5281/zenodo.4767568
Reporting
Adherence to community standards
Yes (indicate where provided
: pag
e
no/section/legend
)
n
/a
MDAR framework
recommends adoption of
discipline
-
specific guidelines,
established and
endorsed through community initiatives. Journals
have their own policy about requiring specific
guidelines and recommendations to complement
MDAR.
State
if relevant guidelines
(eg., ICMJE, MIBBI,
ARRIVE)
have been followed, and whether a checklist
(eg., CONSORT, PRISMA, ARRIVE) is provided with
the
manuscript
.
n/
a