Scientific Data,
Journal Year:
2025,
Volume and Issue:
12(1)
Published: Jan. 26, 2025
Abstracts
The
large-scale
loach
(
Paramisgurnus
dabryanus
;
Cypriniformes:
Cobitidae)
is
primarily
distributed
in
East
Asia.
It
an
important
economic
fish
species
characterized
by
fast
growth,
temperature-dependent
sex
determination
and
the
ability
to
breathe
air.
Currently,
molecular
mechanism
studies
related
some
aspects
such
as
determination,
toxicology,
feed
nutrition,
growth
genetic
evolution
have
been
conducted.
However,
lack
of
a
high-quality
reference
genome
has
hindered
further
research.
In
this
study,
we
performed
PacBio
HiFi
Hi-C
sequencing
on
female
(ZW)
specimen
assembled
first
chromosome-level
loach.
comprises
24
chromosomes,
with
total
length
1.04
Gb,
scaffold
N50
41.7
Mb,
BUSCO
completeness
95.8%,
including
28,311
protein-coding
genes.
These
findings
not
only
provide
new
insights
into
structure
but
also
establish
crucial
point
for
omics
serve
essential
genomic
resource
breeding
programs
species.
GigaScience,
Journal Year:
2025,
Volume and Issue:
14
Published: Jan. 1, 2025
The
scientific
community
has
long
benefited
from
the
opportunities
provided
by
data
reuse.
Recognizing
need
to
identify
challenges
and
bottlenecks
reuse
in
agricultural
research
propose
solutions
for
them,
working
group
was
started
within
AgBioData
consortium
framework.
Here,
we
limitations
of
standards,
metadata
deficiencies,
interoperability,
ownership,
availability,
user
skill
level,
resource
equity
issues,
with
a
specific
focus
on
genomics
research.
We
possible
stakeholders
could
implement
mitigate
overcome
these
provide
an
optimistic
perspective
future
transcriptomics
Nucleic Acids Research,
Journal Year:
2024,
Volume and Issue:
53(D1), P. D30 - D44
Published: Nov. 11, 2024
The
National
Genomics
Data
Center
(NGDC),
which
is
a
part
of
the
China
for
Bioinformation
(CNCB),
offers
comprehensive
suite
database
resources
to
support
global
scientific
community.
Amidst
unprecedented
accumulation
multi-omics
data,
CNCB-NGDC
committed
continually
evolving
and
updating
its
core
through
big
data
archiving,
integrative
analysis
value-added
curation.
Over
past
year,
has
expanded
collaborations
with
international
databases
established
new
subcenters
focusing
on
biodiversity,
traditional
Chinese
medicine
tumor
genetics.
Substantial
efforts
have
been
made
toward
encompassing
broad
spectrum
developing
innovative
enhancing
existing
resources.
Notably,
developed
single-cell
omics
(scTWAS
Atlas),
genome
variation
(VDGE),
health
disease
(CVD
Atlas,
CPMKG,
Immunosenescence
Inventory,
HemAtlas,
Cyclicpepedia,
IDeAS),
biodiversity
biosynthesis
(RefMetaPlant,
MASH-Ocean)
research
tools
(CCLHunter).
All
services
are
publicly
accessible
at
https://ngdc.cncb.ac.cn.
Abstract
ImageGP
is
an
extensively
utilized,
open‐access
platform
for
online
data
visualization
and
analysis.
Over
the
past
7
years,
it
has
catered
to
more
than
700,000
usages
globally,
garnering
substantial
user
feedback.
The
updated
version,
2
(available
at
https://www.bic.ac.cn/BIC
),
introduces
a
redesigned
interface
leveraging
cutting‐edge
web
technologies
enhance
functionality
interaction.
Key
enhancements
include
following:
(i)
Addition
of
modules
format
transformation,
facilitating
operations
such
as
matrix
merging,
subsetting,
transformation
between
long
wide
formats.
(ii)
Streamlined
workflows
with
features
like
preparameter
selection
validation
grouping
parameters
similar
attributes.
(iii)
Expanded
repertoire
functions
analysis
tools,
including
Weighted
Gene
Co‐Expression
Network
Analysis,
differential
gene
expression
analysis,
FASTA
sequence
processing.
(iv)
Personalized
space
uploading
large
sets,
tracking
history,
sharing
reproducible
data,
scripts,
results.
(v)
Enhanced
support
through
simplified
error
debugging
feature
accessible
single
click.
(vi)
Introduction
R
package,
ImageGP,
enabling
local
These
updates
position
versatile
tool
serving
both
wet‐lab
dry‐lab
researchers
expanded
capabilities.
Deleted Journal,
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 7, 2025
Abstract
Small
non‐coding
RNAs
(ncRNAs)
are
functional
molecules
contained
within
extracellular
vesicles
(EVs)
that
modulate
various
physiological
and
pathological
processes.
This
study
provides
a
comprehensive
expression
profile
of
seven
types
small
ncRNAs
in
serum‐
plasma‐derived
EVs
under
conditions.
Both
large
(lEVs)
(sEVs)
contain
high
proportions
miRNAs
(∼28.2%
lEVs
∼20.8%
sEVs)
ribosomal
(∼24.0%
∼19.1%
sEVs).
enriched
with
more
transfer
RNA
(∼38.8%)
than
sEVs,
whereas
sEVs
have
greater
abundance
Y
(∼22.5%).
Notably,
is
abundant
obtained
from
aged
samples
(age
≥60
years),
pattern
not
observed
lEVs.
diverse
serum‐derived
EVs.
There
also
degree
overlap
(>50%)
the
top
100
identified
sEVs.
The
hsa‐miR‐16‐5p,
hsa‐let‐7a‐5p,
hsa‐miR‐142‐3p,
hsa‐miR‐103‐3p
consistently
among
10
highly
expressed
plasma‐
as
well
peripheral
blood
mononuclear
cells.
Serum‐derived
glioblastoma,
breast
cancer,
prostate
gastric
cancer
specific,
miRNAs,
snoRNAs,
nuclear
RNAs,
piRNAs.
These
results
elucidate
patterns
ncRNA
cargoes
derived
serum
plasma
conditions
offer
valuable
insights
for
future
diagnostic
therapeutic
applications.
