Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish

ABSTRACT: Thousands of lncRNAs have been found in zebrafish embryogenesis and adult tissues, but their identification and organogenesis-related function have not elucidated. In this study, high-throughput sequencing was performed at three different organogenesis stages of zebrafish embryos, which were important for zebrafish muscle development. The three stages were 10 hpf (hours post fertilization) (T1), 24 hpf (T2) and 36 hpf (T3).

ORGANISM(S): Danio rerio

PROVIDER: GSE235668 | GEO | 2023/07/19

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish

Project description:Systematic identification of long noncoding RNAs during three key organogenesis stages in zebrafish

| PRJNA986875 | ENA

Human marginal zone B cell development from early T2 progenitors [MZBTraj]

Project description:B cells emerge from the bone marrow as transitional (TS) B cells that differentiate through T1, T2 and T3 stages to become naïve B cells. We have identified a bifurcation of human B cell maturation from the T1 stage forming IgMhi and IgMlo developmental trajectories. IgMhi T2 cells have higher expression of a4b7 integrin and lower expression of IL4 receptor (IL4R) compared to the IgMlo branch and are selectively recruited into gut-associated lymphoid tissue. IgMhi T2 cells also share transcriptomic features with marginal zone B cells (MZB). Lineage progression from T1 cells to MZB via an IgMhi trajectory is identified by pseudotime analysis of scRNA-sequencing data. Reduced frequency of IgMhi gut homing T2 cells is observed in severe SLE and is associated with reduction of MZB and their putative IgMhi precursors. The collapse of the gut-associated MZB maturational axis in severe SLE affirms its existence in health.

2021-01-31 | GSE163602 | GEO

Human marginal zone B cell development from early T2 progenitors [Pooled]

2021-01-31 | GSE163493 | GEO

Liver Chromatin accessibility landscapes during onset of salmon maturation

Project description:We sequenced 12 ATAC-Seq lbraries from four biological replicates before (T1) and after the onset of maturation (T2, T3, T4) from liver. To characterise changes in chromatin state following long light initiation, we defined differentially accessible regions (DARs) where mapping counts differed significantly between T1 and other time points. This revealed a strong early remodelling in the chromatin state landscape, as most DARs were observed at T2 (n=1501) before decreasing in stepwise fashion at T3 (n=477) and T4. The majority of DARs (n=1036 or 57%) exhibit reduced accessibility at T2 compared with T1 and subsequently remained unchanged at later time points (Fig. 5a; Supplementary Figure S14). Similarly, regions that gained accessibility at T2 (n=696 or 38%) also remained unchanged at later timepoints. This left less than 10% of DARs (n=99) that displayed an oscillating pattern following the onset of the maturation. Together, this revealed the ATAC-seq signatures were predominantly stable chromatin state changes.

2020-08-28 | GSE156998 | GEO

Pig experiment Sterksel early antibiotics/stress

Project description:Impact of antibiotics (T2) or antibiotics in combination with stress (T3) in early life on intestinal functioning in pigs on 8, 55, 176 days in jejunum and ileum (blood only day 8) and control pigs (T1) 4 pools consisting of 16 animals were generated per time-point (day 8, 55, 176 after birth) per treatment (T1;control, T2; antibiotics, T3; antibiotics+stress)

2014-09-01 | E-GEOD-53170 | biostudies-arrayexpress

Pig experiment Sterksel early antibiotics/stress

2014-09-01 | GSE53170 | GEO

Systematic proteomics study on the early embryonic development of zebrafish

Project description:Quantitative proteomic data for 10 stages (including 4-cell, 256-cell, 1000-cell, Oblong, Dome, Bud, 16-hpf, 28-hpf, 3-dpf, 5-dpf) of early zebrafish development, each stage corresponds to two sets of biological repeats, and each set of biological repeats corresponds to two sets of technical repeats.

2023-01-10 | PXD039348 |

Effectiveness of hospital-based case management intervention on Chinese colorectal cancer patients

Project description:intervention group was managed for one year by case manager, who organized multidisciplinary team, provided regular assessment, consulting service, and referrals. routine care Primary outcome(s): quality of life was measured at baseline (T0), three days after operation (T1), the first stage (T2-1), middle stage (T2-2) and last stage of chemotherapy (T2-3), and the end of one-year intervention (T3). Study Design: Parallel Non-randomized

| 2660891 | ecrin-mdr-crc

Gene expression in glycerol-grown Yarrowia lipolytica Af4 (DHA producing strain) and Yarrowia lipolytica Po1h (non-producing stain) in different growth phases and different medium conditions

Project description:mRNA was sampled during exponential growth phase (T1), beginning of stationary/production phase (T2), middle of production phase (T3-T4) and end of production phase (T5-T6) strains: Y. lipolytica Af4 - DHA producer (Gemperlein et al., 2019) and Y. lipolytica Po1h - wild type

2024-01-01 | GSE224529 | GEO

Differential expression profiles and functional prediction of tRNA-derived small RNAs in plasma of patients with aortic dissection during deep hypothermic circulatory arrest

Project description:The purpose of this study was to detect the expression profile of tsRNA during deep hypothermia circulatory arrest, and to find possible regulatory factors according to the changes in its expression level, in the hope of providing an effective organ protection strategy for this process.Three blood samples were collected from a central veins line into ethylenediaminetetraacetic acid (EDTA) tubes as follows: T1 (before starting circulatory arrest), T2 (15 min after initiation of DHCA), T3 (after declamping the left common carotid artery and before rewarming). A total of 286 commonly expressed tsRNAs were identified in the T1 and T2 groups, 68 tsRNAs specifically expressed in the T1 group, and 44 tsRNAs specifically expressed in the T2 group. A total of 290 commonly expressed tsRNAs were identified in the T2 and T3 groups, 64 tsRNAs specifically expressed in the T2 group, and 43 tsRNAs specifically expressed in the T3 group. Next, four tsRNAs were selected to be verified by qRT-PCR. In summary, this study innovatively proposed the correlation between the deep hypothermic circulatory arrest process and the expression profile of tsRNA, and evaluated the expression level and regulation mode of tsRNA. A preliminary exploration of its potential biological role in the process of deep hypothermic circulatory arrest has been carried out, which can provide a better basis and a more comprehensive explanation for the organ protection mechanism of deep hypothermic circulatory arrest. And in further research, we are expected to achieve targeted protection of organs by overexpressing or inhibiting the corresponding tsRNA.

2023-04-29 | GSE171909 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data