Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Single cell gene expression analysis of zebrafish body elongation

ABSTRACT: Single cell gene expression analysis of zebrafish body elongation

PROVIDER: PRJNA727493 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR14428600_1.fastq.gz	Fastqsanger.gz
	SRR14428600_2.fastq.gz	Fastqsanger.gz
	SRR14428601_1.fastq.gz	Fastqsanger.gz
	SRR14428601_2.fastq.gz	Fastqsanger.gz
	SRR14428602_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 64

Similar Datasets

Single cell gene expression analysis of zebrafish body elongation

Project description:scRNA-seq analysis was conducted on elongating tail of developping zebrafish. We investigated the cell subpopulaiton during this developping process under purturbation of Wnt, Fgf and BMP signaling pathway.

2021-08-18 | GSE173894 | GEO

Transcription profiling of zebrafish ovary, testis, brain, kidney and whole body to identify gonad-expressed genes and their expression in various organs

Project description:Our knowledge about the molecular regulation of zebrafish gonad development and function is very limited. This study aims to identify gonad-expressed genes in zebrafish and to analyze their expression in various organs. Using our custom ÂGonad Uniclone Microarray v1, we performed a total of 32 hybridizations, using eight target organs with four biological replicates each. The target organs consisted of adult ovary and testis; the brain, kidney and rest-of-body (ie. whole body except the three organs listed earlier) from both male and female zebrafish, were used as controls. For simplicity, rest of body will be regarded as an organ. All targets were hybridized against a pooled common reference consisting of equal amounts of targets from all dissected organs from a single adult male and a single adult female.

2007-12-31 | E-MEXP-1272 | biostudies-arrayexpress

Single-cell transcriptional analysis reveals ILC-like cells in zebrafish

Project description:Transcriptome data from zebrafish single cells from guts from either from Tg(lck:EGFP) rag1-/-mutant or wild-type zebrafish were isolated and single cell suspensions were prepared as described in protocol section. Three zebrafish, per each condition (i.e. zebrafish intraperitoneally injected with PBS, lyophilised Anisakis simplex or inactivated Vibrio anguillarum), were used to collect the total of 12,000 lck+ cells (4000 per zebrafish) for 10x experiment.

2018-11-16 | E-MTAB-7159 | biostudies-arrayexpress

scRNA-seq of fin and body zebrafish melanocytes

Project description:scRNA-seq of fin and body zebrafish melanocytes

| PRJNA753151 | ENA

Activity-assembled nBAF complex mediates rapid immediate early gene transcription by regulating RNA Polymerase II productive elongation

Project description:Signal-dependent RNA Polymerase II (Pol2) productive elongation is an integral component of gene transcription, including those of immediate early genes (IEGs) induced by neuronal activity. However, it remains unclear how productively elongating Pol2 overcome nucleosomal barriers. Using RNAi, three degraders, and several small molecule inhibitors, we show that the mammalian SWI/SNF complex of neurons (neuronal BAF, or nBAF) is required for activity-induced transcription of neuronal IEGs, including Arc. The nBAF complex facilitates promoter-proximal Pol2 pausing, signal-dependent Pol2 recruitment (loading), and importantly, mediates productive elongation in the gene body via interaction with the elongation complex and elongation-competent Pol2. Mechanistically, Pol2 elongation is mediated by activity-induced nBAF assembly (especially, ARID1A recruitment) and its ATPase activity. Together, our data demonstrate that the nBAF complex regulates several aspects of Pol2 transcription and reveal mechanisms underlying activity-induced Pol2 elongation. These findings may offer insights into human maladies etiologically associated with mutational interdiction of BAF functions.

2024-06-18 | PXD052840 | JPOST Repository

Regulated tissue fluidity steers zebrafish body elongation.

Project description:The tailbud is the posterior leading edge of the growing vertebrate embryo and consists of motile progenitors of the axial skeleton, musculature and spinal cord. We measure the 3D cell flow field of the zebrafish tailbud and identify changes in tissue fluidity revealed by reductions in the coherence of cell motion without alteration of cell velocities. We find a directed posterior flow wherein the polarization between individual cell motion is high, reflecting ordered collective migration. At the posterior tip of the tailbud, this flow makes sharp bilateral turns facilitated by extensive cell mixing due to increased directional variability of individual cell motions. Inhibition of Wnt or Fgf signaling or cadherin 2 function reduces the coherence of the flow but has different consequences for trunk and tail extension. Modeling and additional data analyses suggest that the balance between the coherence and rate of cell flow determines whether body elongation is linear or whether congestion forms within the flow and the body axis becomes contorted.

| S-EPMC3561786 | biostudies-literature

Analysis of single CD41 cell transcriptomes from Zebrafish

Project description:Transcriptome data from individual CD41 expressing cells isolated from kidney and heart of zebrafish. CD41 is a marker both for HSCs and thrombocytes, and with this data we study thrombocyte development as a continuous process. Single cell transcriptomes are matched with flourescence of a CD41:GFP reporter.

2016-01-08 | E-MTAB-3947 | biostudies-arrayexpress

Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 1]

Project description:Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 1]

| PRJNA745345 | ENA

Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 2]

Project description:Nr6a1 controls axially-restricted body elongation, patterning and lineage allocation [dataset 2]

| PRJNA748236 | ENA

Analysis of single CD41 cell transcriptomes from Zebrafish

Project description:Analysis of single CD41 cell transcriptomes from Zebrafish

| PRJEB11748 | ENA