Plant Diversity,
Год журнала:
2024,
Номер
46(3), С. 372 - 385
Опубликована: Апрель 3, 2024
Plant
morphogenesis
relies
on
precise
gene
expression
programs
at
the
proper
time
and
position
which
is
orchestrated
by
transcription
factors
(TFs)
in
intricate
regulatory
networks
a
cell-type
specific
manner.
Here
we
introduced
comprehensive
single-cell
transcriptomic
atlas
of
Arabidopsis
seedlings.
This
result
meticulous
integration
63
previously
published
scRNA-seq
datasets,
addressing
batch
effects
conserving
biological
variance.
spans
broad
spectrum
tissues,
including
both
below-
above-ground
parts.
Utilizing
rigorous
approach
for
cell
type
annotation,
identified
47
distinct
types
or
states,
largely
expanding
our
current
view
plant
compositions.
We
systematically
constructed
uncovered
key
regulators
that
act
coordinated
manner
to
control
expression.
Taken
together,
study
not
only
offers
extensive
exploration
serves
as
valuable
resource,
but
also
provides
molecular
insights
into
gene-regulatory
varies
from
different
types.
Andrology,
Год журнала:
2023,
Номер
11(6), С. 1157 - 1162
Опубликована: Янв. 30, 2023
Abstract
Background
The
development
of
single‐cell
sequencing
technology
has
expanded
the
understanding
cell
heterogeneity
and
disease
progression
in
male
genitourinary
system.
However,
complex
processing
unprofessional
analytical
annotations
limit
daily
use
widely
sharing
published
datasets.
Objectives
Single‐cell
data
male‐specific
tissues
organs.
Materials
methods
were
downloaded
from
studies
processed
based
on
Seurat
R
package,
including
quality
control,
clustering,
reduction
graph
generation,
type
annotation
differentiated
by
referring
to
related
paper
or
recognized
markers.
Input
visual
results
output
through
Shiny
which
was
loaded
into
remote
server.
Results
current
version
Male
Health
Atlas
database
includes
two
species
(human
mouse),
five
organs
(testis,
epididymis,
vas
deferens,
corpus
cavernosum,
prostate),
eight
major
types,
with
a
total
57
samples
258,428
profiles.
divided
main
parts:
Cell
Clustering
Gene
Display.
In
section,
visitors
are
free
change
dimensionality
(
t
‐distributed
stochastic
neighbor
embedding,
uniform
manifold
approximation
projection),
color
palette,
(cell
sample
type).
Display
section
reduced
dimension
scatter
plot,
violin
bubble
plot.
Visitors
can
easily
view
expression
characteristics
single
multiple
genes,
compare
differences
between
different
types
groups.
Discussion
conclusion
is
first
website
field
andrology
reproduction,
providing
researchers
resources
an
accessible
tool.
freely
available
at
http://malehealthatlas.cn/
.
Nature Communications,
Год журнала:
2022,
Номер
13(1)
Опубликована: Июль 25, 2022
Abstract
The
rapid
development
of
high-throughput
single-cell
RNA
sequencing
technology
offers
a
good
opportunity
to
dissect
cell
heterogeneity
animals.
A
large
number
organism-wide
atlases
have
been
constructed
for
vertebrates
such
as
Homo
sapiens
,
Macaca
fascicularis
Mus
musculus
and
Danio
rerio
.
However,
an
intermediate
taxon
that
links
mammals
more
ancient
origin
is
still
lacking.
Here,
we
construct
the
first
Xenopus
landscape
date,
including
larval
adult
organs.
Common
lineage-specific
transcription
factors
identified
in
vertebrates,
fish,
amphibians
mammals.
comparison
erythrocytes
identifies
stage-specific
hemoglobin
subtypes,
well
common
type
cluster
containing
both
hemoglobin,
mainly
at
NF59.
In
addition,
lineages
originating
from
all
three
layers
exhibits
antigen
processing
presentation
during
metamorphosis,
indicating
regulatory
mechanism
metamorphosis.
Overall,
our
study
provides
large-scale
resource
research
on
metamorphosis
Frontiers in Genetics,
Год журнала:
2023,
Номер
13
Опубликована: Янв. 4, 2023
Over
the
past
decade,
with
development
of
high-throughput
single-cell
sequencing
technology,
omics
has
been
emerged
as
a
powerful
tool
to
understand
molecular
basis
cellular
mechanisms
and
refine
our
knowledge
diverse
cell
states.
They
can
reveal
heterogeneity
at
different
genetic
layers
elucidate
their
associations
by
multiple
analysis,
providing
more
comprehensive
map
biological
regulatory
networks.
In
post-GWAS
era,
influencing
human
diseases
will
be
further
elucidated
omics.
This
review
mainly
summarizes
trend
involves
technologies,
multi-omics
data
integration
methods,
applications
in
various
organs
diseases,
classic
laboratory
lines,
animal
disease
models.
The
some
perspectives
for
elucidating
constructing
JACC Basic to Translational Science,
Год журнала:
2024,
Номер
9(3), С. 380 - 395
Опубликована: Янв. 24, 2024
To
solve
the
clinical
transformation
dilemma
of
lamin
A/C
(LMNA)-mutated
dilated
cardiomyopathy
(LMD),
we
developed
an
LMNA-mutated
primate
model
based
on
similarity
between
phenotype
primates
and
humans.
We
screened
out
patients
with
LMD
compared
data
TTN-mutated
mutation-free
to
obtain
unique
phenotype.
After
establishment
LMNA
c.357-2A>G
model,
were
continuously
observed
for
48
months,
echocardiographic,
electrophysiological,
histologic,
transcriptional
recorded.
The
was
found
highly
simulate
LMD.
In
addition,
shared
a
similar
natural
history
Abstract
Cell‐specific
transcriptional
regulatory
networks
(TRNs)
play
vital
roles
in
plant
development
and
response
to
environmental
stresses.
However,
traditional
single‐cell
mono‐omics
techniques
are
unable
directly
capture
the
relationships
dynamics
between
different
layers
of
molecular
information
within
same
cells.
While
advanced
algorithm
facilitates
merging
scRNA‐seq
scATAC‐seq
datasets,
accurate
data
integration
remains
a
challenge,
particularly
when
investigating
cell‐type‐specific
TRNs.
By
examining
gene
expression
chromatin
accessibility
simultaneously
16,670
Arabidopsis
root
tip
nuclei,
TRNs
reconstructed
that
govern
under
osmotic
stress.
In
contrast
commonly
used
computational
at
cell‐type
level,
12,968
peak‐to‐gene
linkage
is
captured
bona
fide
level
construct
an
unprecedented
resolution.
Furthermore,
datasets
allow
more
accurately
reconstruct
coordinated
changes
states
during
cellular
state
transition.
During
development,
initial
cells
precedes
expression,
suggesting
may
prime
for
subsequent
differentiation
steps.
Pseudo‐time
trajectory
analysis
reveal
stress
can
shift
functional
trichoblast.
Candidate
stress‐related
gene‐linked
cis‐regulatory
elements
(gl‐cCREs)
as
well
potential
target
genes
also
identified,
uncovered
large
heterogeneity
Neutrophils
are
important
immune
cells
act
as
the
body's
first
line
of
defense
against
infection
and
respond
to
diverse
inflammatory
cues.
Many
studies
have
demonstrated
that
neutrophils
display
plasticity
in
diseases
cancers.
Clarifying
role
neutrophil
heterogeneity
cancers
will
contribute
development
novel
treatment
strategies.
In
this
review,
we
presented
a
review
on
understanding
from
traditional
perspective
high-resolution
viewpoint.
A
growing
body
evidence
has
confirmed
double-edged
tumors.
This
may
be
due
lack
precise
specific
subsets
disease.
Thus,
elucidating
involved
would
benefit
precision
medicine.
Thusly,
summarized
relevance
actions
comprehensively.
Meanwhile,
also
discussed
potential
intervention
strategy
for
neutrophils.
is
intended
deepen
our
cancers,
while
hold
promise
neutrophil-related
diseases.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Март 11, 2024
Hormones
mediate
long-range
cell
communication
and
play
vital
roles
in
physiology,
metabolism,
health.
Traditionally,
endocrinologists
have
focused
on
one
hormone
or
organ
system
at
a
time.
Yet,
signaling
by
its
very
nature
connects
cells
of
different
organs
involves
crosstalk
hormones.
Here,
we
leverage
the
organism-wide
single
transcriptional
atlas
non-human
primate,
mouse
lemur
(Microcebus
murinus),
to
systematically
map
source
target
for
84
classes
This
work
uncovers
previously-uncharacterized
sites
regulation,
shows
that
hormonal
network
is
densely
connected,
decentralized,
rich
feedback
loops.
Evolutionary
comparisons
genes
their
expression
patterns
show
better
models
human
than
mouse,
both
genomic
transcriptomic
levels,
reveal
primate-specific
rewiring
hormone-producing/target
cells.
complements
scale
resolution
classical
endocrine
studies
sheds
light
primate
regulation.
