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Items: 1 to 20 of 258

1.

mRNA seq of WT and tp53 e7/e7 mutant in zebrafish intestine with or without gut microbiota.

(Submitter supplied) In order to explore host factor provided by tp53 e7/e7 mutants that supports the colonization of specific microbiota, comparative transcriptomic analyses of intestines of WT vs. tp53 mutants or CV vs. GF conditions at 7 dpf were performed.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
8 Samples
Download data: TXT
Series
Accession:
GSE150376
ID:
200150376
2.

PCB126 exposure induced DNA methylation and gene expression changes in adult zebrafish testis

(Submitter supplied) The objective of this study is to determine the effects of pre-conceptional exposure to environmental chemicals on DNA methylation and gene expression in testis. We used a dioxin-like PCB (3, 3’, 4, 4’, 5-pentachlorobiphenyl; PCB126) as a model environmental chemical because the mechanism of action is well-characterized, involving activation of aryl hydrocarbon receptor, a ligand-activated transcription factor. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platforms:
GPL14875 GPL18413
34 Samples
Download data: TXT
Series
Accession:
GSE190741
ID:
200190741
3.

Integrated molecular analysis identifies new developmental pericyte markers in zebrafish

(Submitter supplied) We performed single cell and bulk RNA-seq analyses on pdgfrb-positive cells to identify candidate pericyte-expressed genes. For bulk RNA-seq, we used wild type pdgfrb-positive samples from Series GSE152759 (GEO ID: GSM4625924, GSM4625925, GSM4625926) for comparison to mutant pdgfrb-positive cells in this Series. These cells had originally been isolated in parallel.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL21741 GPL14875
5 Samples
Download data: CSV, MTX, TSV
Series
Accession:
GSE176129
ID:
200176129
4.

Four-month-old zebrafish brain transcriptome analysis of mitofusin 2 (mfn2) loss-of-function mutation (hu3528 allele) homozygous, heterozygous, and wild type siblings

(Submitter supplied) An assessment of brain transcriptome differences between zebrafish siblings homozygous, heterozygous, and wild type for a loss-of-function mutation in mfn2.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
18 Samples
Download data: TXT
Series
Accession:
GSE161117
ID:
200161117
5.

Specialized injury-induced serotonergic neurons promote circuit reorganization and function restoration after spinal cord injury in zebrafish

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
60 Samples
Download data
Series
Accession:
GSE182911
ID:
200182911
6.

Next Generation Sequencing of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury

(Submitter supplied) The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish intraspinal serotonergic neurons in the injury segment and distal segments after spinal cord injury. Bulk RNA-Seq samples of ISNs from the injury area and residual segments respectively were FAC-sorted from Tg(tph2:GFP) line. Total RNA was isolated using SMART-SeqTM v4 UltraTM Low Input RNA Kit for Sequencing (Clontech). more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
11 Samples
Download data: TXT
Series
Accession:
GSE182869
ID:
200182869
7.

Next Generation Sequencing of zebrafish spinal cord transcriptomes before and after injury

(Submitter supplied) The goals of this study is to compare transcriptome profiles (RNA-seq) of zebrafish spinal cord before and after injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one, two, four, and six weeks post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries (N=4-5) were subjected to Illumina sequencing. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
49 Samples
Download data: TXT
Series
Accession:
GSE182868
ID:
200182868
8.

Sulfonamide functional head group drives developmental toxicity of short-chain per- and polyfluorolkyl substances

(Submitter supplied) Purpose: The goals of this study are to investigate developmental toxicity and hazard potential of a short-chain PFAS homologous series in zebrafish, specifically interrogating the impact of different functional head groups. Developmental toxicity findings were supplemented with investigations into transcriptom-wide effects of body burdens following PFAS exposures. Methods: For developmental toxicity assessments, dechorionated embryonic zebrafish were statically exposed at 8 hours post fertilization (hpf) to either vehicle control (0.5% methanol) or to FBSA, PFBS, PFPeA, or 4:2 FTS across a range of concentrations (1-100 µM, normalized to 0.5% methanol) in 96-well plate format. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
15 Samples
Download data: XLSX
Series
Accession:
GSE186576
ID:
200186576
9.

Sequencing of Danio rerio skin for 2 age groups

(Submitter supplied) Comparison of Danio rerio skin for 2 age groups treated with Rotenone. The RNA-seq data comprises two age groups treated with different Rotenone dose levels. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
26 Samples
Download data: XLS
Series
Accession:
GSE102433
ID:
200102433
10.

Sequencing of Danio rerio liver for 2 age groups

(Submitter supplied) Comparison of Danio rerio liver for 2 age groups treated with Rotenone. The RNA-seq data comprisess two age groups treated with Rotenone. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
24 Samples
Download data: XLS
Series
Accession:
GSE102428
ID:
200102428
11.

Sequencing of Danio rerio brain for 2 age groups after Rotenone treatment

(Submitter supplied) Comparison of Danio rerio brain for 2 age groups treated with Rotenone. The RNA-seq data comprises two age groups treated with different Rotenone dose levels. Jena Centre for Systems Biology of Ageing - JenAge (www.jenage.de)
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
26 Samples
Download data: XLS
Series
Accession:
GSE102425
ID:
200102425
12.

The RNA helicase Ddx21 controls Vegfc-driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53-p21 signalling

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL14875 GPL18573
20 Samples
Download data
Series
Accession:
GSE180330
ID:
200180330
13.

The RNA helicase Ddx21 controls Vegfc-driven developmental lymphangiogenesis by balancing endothelial cell ribosome biogenesis and p53-p21 signalling [zebrafish]

(Submitter supplied) The development of a differentiated and functional vasculature requires coordinated control of cell fate specification, lineage differentiation and vascular network growth. Cellular proliferation is spatiotemporally regulated in developing vessel networks but how this is achieved and differentially controlled in specific lineages is unknown. Using a zebrafish forward genetic screen for mutants that form blood vessels but fail to form lymphatic vessels, we uncovered a mutant for the RNA helicase Ddx21. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
8 Samples
Download data: CSV
Series
Accession:
GSE158566
ID:
200158566
14.

5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing; Other; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL14875 GPL24995
19 Samples
Download data: BW
Series
Accession:
GSE181684
ID:
200181684
15.

5’ half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos [small RNA-Seq, ssDRIP-seq]

(Submitter supplied) 5’tRFls are small tRNA fragments derived from 5’ half of mature tRNAs. However, it is unknown whether 5’tRFls could feed back to regulate tRNA biogenesis. Here we show that 5’tRFlGly/GCC and 5’tRFlGlu/CTC function to promote transcription of corresponding tRNA genes and are essential for vertebrate early embryogenesis. During zebrafish embryogenesis, dynamics of 5’tRFlGly/GCC and 5’tRFlGlu/CTC levels correlates with that of tRNAGly/GCC and tRNAGlu/CTC levels. more...
Organism:
Danio rerio
Type:
Non-coding RNA profiling by high throughput sequencing; Other
Platforms:
GPL24995 GPL14875
13 Samples
Download data: BW, TXT, XLSX
16.

Next Generation Sequencing Based RNAseq Analysis of lri25-/- mutant zebrafish larvae at 5 dpf.

(Submitter supplied) Gene expression profiles in lri25 mutant zebrafish larvae at 5 dpf based on the RNAseq data.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
2 Samples
Download data: CSV
Series
Accession:
GSE181602
ID:
200181602
17.

Genetic compensation for cilia defects in cep290/NPHP6 mutants by upregulation of cilia-associated small GTPases

(Submitter supplied) Mutations in CEP290, a large multidomain coiled coil protein, are associated with multiple cilia-associated syndromes. Over 130 CEP290 mutations have been linked to a wide spectrum of human ciliopathies, raising the question of how mutations in a single gene cause different disease syndromes. In zebrafish the expressivity of cep290 deficiencies were linked to the type of genetic ablation: acute cep290 morpholino knockdown caused severe cilia-related phenotypes while defects in a Crispr/Cas9 genetic mutant were restricted to photoreceptor defects. more...
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
9 Samples
Download data: TXT, XLSX
Series
Accession:
GSE175491
ID:
200175491
18.

Comparitive transcriptome analysis of two zebrafish mutants goosepimples/myovb and romeharsha

(Submitter supplied) This dataset comprises RNA-Seq data from two zebrafish mutants and their respective sibling controls. These mutants show trafficking defects leading to accumuation of early and late endocytic vesicles and rounding up in the periderm. The goosepimples mutation has been identified as a null form of MyoVb, an actin based motor. Differential expression analysis suggests upregulation of grainyhead familiy transcription factors Grhl1 and Grhl3 along with various adhesion associated genes.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
4 Samples
Download data: XLSX
Series
Accession:
GSE173649
ID:
200173649
19.

TCDD exposure in control and wfikkn1mutant zebrafish at 48 hpf

(Submitter supplied) This experiment investigates the role of a novel AHR-regulated gene on the global transcriptome in 48 hpf zebrafish exposed to 0.1% DMSO or 1 ng/mL TCDD.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platform:
GPL14875
16 Samples
Download data: TXT, XLSX
Series
Accession:
GSE172418
ID:
200172418
20.

RNA seq data examining response to chemical treatment to build the first gene co-expression network of zebrafish

(Submitter supplied) This study combines RNA seq data from a number of different expeirments examining response to chemical treatment to build the first gene co-expression network of zebrafish. We interrogate this network to determine how the transcriptomic map responds to different types of chemicals and what pathways and processes are critical to chemical response
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL14875 GPL23274
170 Samples
Download data: CSV
Series
Accession:
GSE171944
ID:
200171944
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