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Items: 1 to 20 of 54600

1.

On the requirement for cell division in cell differentiation during early embryo development [II]

(Submitter supplied) Paper abstract: As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single-cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. more...
Organism:
Danio rerio
Type:
Other
Platform:
GPL24995
1 Sample
Download data: CSV, H5AD, TSV, XLSX
Series
Accession:
GSE269848
ID:
200269848
2.

On the requirement for cell division in cell differentiation during early embryo development [I]

(Submitter supplied) As tissues develop, cells divide and differentiate concurrently. Conflicting evidence shows that cell division is either dispensable or required for formation of cell types. To determine the role of cell division in differentiation, we arrested the cell cycle in zebrafish embryos using two independent approaches and profiled them at single-cell resolution. We show that cell division is dispensable for differentiation of all embryonic tissues during initial cell type differentiation from early gastrulation to the end of segmentation. more...
Organism:
Danio rerio
Type:
Other
Platform:
GPL20828
12 Samples
Download data: CSV, H5AD, TSV, TXT
Series
Accession:
GSE269784
ID:
200269784
3.

A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio; Homo sapiens
Type:
Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platforms:
GPL21741 GPL20301 GPL20828
40 Samples
Download data: NARROWPEAK, TSV
Series
Accession:
GSE213360
ID:
200213360
4.

A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [SORT-seq]

(Submitter supplied) Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein (TIE:EGFP). EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
12 Samples
Download data: TSV
Series
Accession:
GSE213359
ID:
200213359
5.

A chronic signaling TGFb zebrafish reporter identifies immune response in melanoma [RNA-seq, ZMEL]

(Submitter supplied) Developmental signaling pathways associated with growth factors such as TGFb are commonly dysregulated in melanoma. Here we identified a human TGFb enhancer that was specifically activated in melanoma cells treated with TGFB1 ligand. We generated stable transgenic zebrafish with this enhancer driving green fluorescent protein (TIE:EGFP). EGFP was not expressed in normal melanocytes or early melanomas but was expressed in spatially distinct regions of mature melanomas. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL21741
6 Samples
Download data: TXT
Series
Accession:
GSE213328
ID:
200213328
6.

Single-cell analysis of innate spinal cord regeneration identifies intersecting modes of neuronal repair

(Submitter supplied) Adult zebrafish have an innate ability to recover from severe spinal cord injury. Here, we report a comprehensive single nuclear RNA sequencing atlas that spans 6 weeks of regeneration. We identify cooperative roles for adult neurogenesis and neuronal plasticity during spinal cord repair. Neurogenesis of glutamatergic and GABAergic neurons restores the excitatory/inhibitory balance after injury. In addition, a transient population of injury-responsive neurons (iNeurons) show elevated plasticity between 1 and 3 weeks post-injury. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
8 Samples
Download data: MTX, TSV
Series
Accession:
GSE235395
ID:
200235395
7.

Rbpms2 promotes female fate upstream of the nutrient sensing Gator2 complex component, Mios

(Submitter supplied) Reproductive success relies on proper establishment and maintenance of biological sex. In many animals, including mammals, the primary gonad is initially ovary in character. We previously showed the RNA binding protein (RNAbp), Rbpms2, is required for ovary fate in zebrafish. Here, we identified Rbpms2 targets in oocytes(Rbpms2-bound oocyte RNAs; rboRNAs). We identify Rbpms2 as a translational regulator ofrboRNAs, which include testis factors and ribosome biogenesis factors. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
10 Samples
Download data: CSV, XLSX
Series
Accession:
GSE254850
ID:
200254850
8.

scRNA-seq reveals the diversity of the developing cardiac cell lineage and molecular players in heart rhythm regulation

(Submitter supplied) We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
4 Samples
Download data: CSV, MTX, TSV
Series
Accession:
GSE234216
ID:
200234216
9.

Pioneer neurons are molecularly distinct, and their axon targeting is regulated by retinoic acid signaling (WT 30 h)

(Submitter supplied) During nervous system development, pioneer neurons are the first to extend their axons into target tissues, creating a scaffold for follower neurons. Despite years of study, whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line (pLL) sensory neurons during axon growth using single-cell RNA sequencing (scRNA-seq) revealed that pioneer and follower neurons are transcriptionally distinct. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
1 Sample
Download data: MTX, TSV
Series
Accession:
GSE266312
ID:
200266312
10.

Pioneer neurons are molecularly distinct, and their axon targeting is regulated by retinoic acid signaling

(Submitter supplied) During nervous system development, pioneer neurons are the first to extend their axons into target tissues, creating a scaffold for follower neurons. Despite years of study, whether pioneer neurons are a molecularly distinct population is unknown. Analysis of zebrafish posterior lateral line (pLL) sensory neurons during axon growth using single-cell RNA sequencing (scRNA-seq) revealed that pioneer and follower neurons are transcriptionally distinct. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
3 Samples
Download data: MTX, TSV
Series
Accession:
GSE264323
ID:
200264323
11.

RNA-seq analysis of the WT and bcas2-KO zebrafish embryos at 3 dpf

(Submitter supplied) The splicing factor Bcas2 is involved in several biological processes including tumorigenesis, gametogenesis, and hematopoiesis. The alternative splicing events and downstream genes regulated by Bcas2 have not yet been investigated at the transcriptome level in zebrafish. In this study, we conducted RNA-sequencing analysis on the WT and bcas2 knockout zebrafish embryos (3 dpf) to identify the global differentially expressed genes (DEGs) and differential splicing events (DSEs). more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
6 Samples
Download data: TXT
Series
Accession:
GSE246374
ID:
200246374
12.

Validation of sgRNAs against acaa2 and tlr4 in zebrafish.

(Submitter supplied) To study the knockout efficiency of Acaa2 and TLR4 in vivo.
Organism:
Danio rerio
Type:
Other
Platform:
GPL24995
20 Samples
Download data: CSV
Series
Accession:
GSE203490
ID:
200203490
13.

tp53 R217H and R242H Mutant Zebrafish Display Dysfunctional p53 Hallmarks and Recapitulate LFS Phenotypes [WGBS]

(Submitter supplied) Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with a highly penetrant and diverse tumor spectrum characterized by germline mutations in the TP53 tumor suppressor gene. To better understand how TP53 mutations predispose individuals with LFS to cancer development, we characterized tp53 R217H and R242H zebrafish lines as the first zebrafish p53 hotspot mutants (human R248 and R273H). more...
Organism:
Danio rerio
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL24995
12 Samples
Download data: BED, TXT
Series
Accession:
GSE268283
ID:
200268283
14.

Deficiency of P2RY11 causes narcolepsy and attenuates recruitment of neutrophils and macrophages of inflammatory response in zebrafish

(Submitter supplied) Purinergic receptor P2Y11, a G protein-coupled receptor that is stimulated by the endogenous ATP, has been demonstrated to be related with the chemotaxis of granulocytes, apoptosis of neutrophils, and secretion of cytokines in vitro. P2Y11 mutations were associated with narcolepsy. However, little is known about the roles of P2RY11 in the occurrence of narcolepsy and inflammatory response in vivo. In this study, we generated zebrafish P2Y11 mutant by CRISPR/Cas9 genome editing and performed gene expression profiling analysis.To analyze the P2RY11 function, we performed GO term analysis of the up-regulated and down-regulated DE genes of P2RY11-8bp versus their WT controls. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL24995
6 Samples
Download data: XLSX
Series
Accession:
GSE264674
ID:
200264674
15.

R-loop landscapes during parental-to-zygotic transition in zebrafish

(Submitter supplied) The R-loop is a common chromatin feature presented from prokaryotic to eukaryotic genomes and has been revealed to be involved in multiple cellular processes. Here, we developed a novel R-loop profiling technique, ULI-ssDRIP-seq, to decte global R-loops from a limited number of cells. Based on this method, we profiled the R-loop landscapes during parental-to-zygotic transition and early development regulatory in zebrafish, and revealed a series of important characters of R-loops.
Organism:
Escherichia coli; synthetic construct; Arabidopsis thaliana; Danio rerio
Type:
Other; Expression profiling by high throughput sequencing
4 related Platforms
60 Samples
Download data: BW
Series
Accession:
GSE183453
ID:
200183453
16.

Large-scale screen of novel zebrafish retinal ganglion cell ablation model reveals genetic regulation of retinal regeneration is context specific

(Submitter supplied) Many genes are known to regulate Müller glia (MG)-dependent retinal regeneration following widespread tissue damage. Conversely, genes controlling regeneration following limited retinal cell loss, per degenerative disease, are undefined. Studying regeneration in the context of selective cell loss is important as evidence suggests injury specifics inform the regenerative process. Here, transgenic zebrafish enabling inducible selective retinal ganglion cell (RGC) ablation were combined with single cell multiomics and CRISPR/Cas9-based knockout methods to screen 101 genes for effects on RGC regeneration. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL24995
20 Samples
Download data: H5, MTX, TBI, TSV
Series
Accession:
GSE268179
ID:
200268179
17.

Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18413
28 Samples
Download data
Series
Accession:
GSE175447
ID:
200175447
18.

Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos [RNA-seq]

(Submitter supplied) Brg1 and Brm function as alternative core enzymatic ATPases of SWI/SNF complex in vertebrates, with clear homologs in zebrafish. Brg1 (but not Brm) is required for early cleavage-stage transcription in mice, but where and how Brg1 or Brm impact chromatin in early embryos remains unexplored. Here, we utilize zebrafish embryos to provide the first simultaneous genome-wide profiling of Brg1 and Brm occupancy in any organism/cell type, alongside our profiling of open chromatin and RNA polymerase II. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL18413
5 Samples
Download data: XLSX
Series
Accession:
GSE175446
ID:
200175446
19.

Distinctive roles for the chromatin remodeling ATPases Brg1 and Brm in early zebrafish embryos [ChIP-seq]

(Submitter supplied) Brg1 and Brm function as alternative core enzymatic ATPases of SWI/SNF complex in vertebrates, with clear homologs in zebrafish. Brg1 (but not Brm) is required for early cleavage-stage transcription in mice, but where and how Brg1 or Brm impact chromatin in early embryos remains unexplored. Here, we utilize zebrafish embryos to provide the first simultaneous genome-wide profiling of Brg1 and Brm occupancy in any organism/cell type, alongside our profiling of open chromatin and RNA polymerase II. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by high throughput sequencing
Platform:
GPL18413
23 Samples
Download data: BW
Series
Accession:
GSE175444
ID:
200175444
20.

Small molecule ML233 is a direct inhibitor of tyrosinase function and reduces melanoma proliferation

(Submitter supplied) Melanogenesis is the biological process regulating the synthesis of melanin pigments in melanocytes. Defective melanogenesis is associated with numerous human skin diseases, including, but not limited to, albinism, vitiligo, melasma, hypo- and hyperpigmentation disorders. Tyrosinase is the rate-limiting enzyme controlling melanogenesis, and hence tremendous efforts have been made to identify potent and safe inhibitors of tyrosinase function. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL20828
24 Samples
Download data: TXT
Series
Accession:
GSE268076
ID:
200268076
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