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.
Materials and Methods
mH2A1 (Abcam Cat#
ab232602
,
RRID:AB_2716576)
H3K27ac
(Active Motif Cat#
39133, RRID:AB_2561016)
H3K27me2 (Cell Signaling Cat#
9728BF,
RRID:AB_1281338)
H3K27me3 (Cell Signaling Cat#
9733BF,
RRID:AB_2616029)
H3K4me2 (Cell Signaling Cat#
9725BF,
RRID:AB_10205451)
H3K9me3 (Diagenode Cat#
MAb
-
146
-
050)
H4K20me3 (A
ctive Motif Cat#
39671
, RRID:AB_2650526
)
MeCP2 (Cell Signaling Cat#
3456BF
, RRID:AB_2143849
)
RNA polymerase II (phospho S5) (Abcam Cat#
ab5408
,
RRID:AB_304868
)
SF3a66 (Abcam Cat#
ab77800
,
RRID:AB_2186364)
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
Materials and Methods
E14 m
ouse
ES
cells
(E14Tg2a.4) (
RRID:MMRRC_015890
-
UCD
)
NIH/3T3 cells (ATCC CRL
-
1658)
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
Materials and Methods
6
-
7
-
week
-
old
wild
-
type
C57BL/6J female mice
from
The
Jackson Laboratory
(
Stock No: 000664 | B6
)
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
n/a
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
Materials and Methods
The DNA seqFISH+ experiment was replicated three
times
.
Define whether data describe technical or biological
replicates
Materials and Methods
Data describe biological replicates.
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.
The animal experiment was performed by following
the
IACUC protocol (
IA18
-
1763
).
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.
Details
for the exclusion criteria
are described in
Materials and Methods
.
Statistics
Yes (indicate where provided
:
page
no/section/legend
)
n/a
Describe
statistical tests used and justify choice of
tests.
D
etails
for statistical tests used (
two
-
sided Wilcoxon’s
signed rank
-
sum test
)
are described in
Materials and
Methods
.
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.
The newly created datasets
are
publicly available.
If data are publicly available,
provide
accessi
on
number in
repository or DOI
or
URL.
https://
doi
.org/
10.5281/zenodo.4708112
If
publicly available data are reused,
provide
accession number in repository or DOI or URL, where
possible.
Materials and Methods
Hi
-
C (
NCBI GEO accession
number
GSE35156
)
CTCF, Rad21 ChIP
-
seq (
NCBI
GEO accession
number
GSE35140
)
H3K27me3 scChIP
-
seq (NCBI
GEO accession
number
GSE152020
)
scRNA
-
seq (
NCBI GEO
accession
number
GSE71585
)
E14 DNA seqFISH+
(https://
doi
.org/
10.5281/zenodo.3735328
)
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
publicly
available.
If code is publicly available,
provide
accessi
on
number in repository, or DOI or URL.
https://doi.org/10.5281/zenodo.5507507
associated
with a Github repository
https://github.com/CaiGroup/dna
-
seqfish
-
plus
-
tissue
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