Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ScRNAseq libraries of pooled kidney samples from wild type (ZF1) versus CRISPR-targeted renin knockout (ZF2) zebrafish

ABSTRACT: Libraries were made to compare the transcriptome of renin lineage cells (RLCs) from wild-type versus ren knockout zebrafish kidneys. RLCs were FAC sorted from pooled kidneys of ren+/+ or ren-/- zebrafish, which carried ren:RFP and acta2:EGFP reporter genes, allowing the isolation of renin-expressing cells and smooth muscle cells.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Danio rerio

SUBMITTER: Linda Mullins

PROVIDER: E-MTAB-11079 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Comparative Studies of Renin-Null Zebrafish and Mice Provide New Functional Insights.

Hoffmann Scott S Mullins Linda L Rider Sebastien S Brown Cara C Buckley Charlotte B CB Assmus Adrienne A Li Ziwen Z Sierra Beltran Mariana M Henderson Neil N Del Pozo Jorge J De Goes Martini Alexandre A Sequeira-Lopez Maria Luisa S MLS Gomez R Ariel RA Mullins John J

Hypertension (Dallas, Tex. : 1979) 20220110 3

<h4>Background</h4>The renin-angiotensin system is highly conserved across vertebrates, including zebrafish, which possess orthologous genes coding for renin-angiotensin system proteins, and specialized mural cells of the kidney arterioles, capable of synthesising and secreting renin.<h4>Methods</h4>We generated zebrafish with CRISPR-Cas9-targeted knockout of renin (<i>ren</i><sup>-/-</sup>) to investigate renin function in a low blood pressure environment. We used single-cell (10×) RNA sequenci ...[more]

PMID: 35000430

Similar Datasets

Single-nucleus RNA-seq of liver tissue of 3 months old mice to investigate crosstalk between ploidy and zonation

Project description:Single-nucleus RNA-seq-2 method that allows deep characterization of nuclei isolated from frozen archived tissues. We have used this approach to characterize the transcriptional profile of individual hepatocytes with different levels of ploidy. This method has the potential to explore archived samples, for instance to study the development and progression of disease in complex tissues. To illustrate the potential of this method, we have deeply characterized the cellular heterogeneity driven by spatial distribution and different levels of ploidy in the young adult mouse liver.

2021-05-06 | E-MTAB-10223 | biostudies-arrayexpress

Single-cell RNA-seq of the human fetal lateral ganglionic eminence at 7, 9 and 11 post-conceptional weeks

Project description:Single-cell RNA-seq of the LGE between 7 and 11 pcw was used to uncover the different cell populations of the developing human striatum and how cells transition from early progenitors to mature medium spiny neuron (MSNs) together with the discovery of their unique coding and non-coding transcriptional signature.

2021-05-13 | E-MTAB-8894 | biostudies-arrayexpress

Single-cell RNA-seq of telencephalic organoids from healthy CTRL and HD (Huntington’s disease) hESC (RUES2) grown as mono-culture or co-culture of chimeric organoids

Project description:Use of single-cell transcriptomics to test early HD selective vulnerability by comparing CTRL and HD telencephalic organoids at day 45 and 120 of differentiation. To test the influence and the interactions between healthy and HD cells, chimeric organoids composed of CTRL and HD cells juxtaposed within the same organoid were grown and analyzed by scRNAseq at day 120.

2024-07-02 | E-MTAB-12924 | biostudies-arrayexpress

Single-cell transcription profiling human dorsal forebrain organoids treated with Hyper-IL-6

Project description:We performed single-cell RNA sequencing of dorsal forebrain organoids at day 53 of differentiation upon treatment with Hyper-IL-6. The study aimed at investigation of the effects of Hyper-IL-6 on transcriptional profiles of dorsal forebrain organoids at single-cell level.

2023-03-08 | E-MTAB-12743 | biostudies-arrayexpress

scRNAseq (10x) of mpk cells grown on plastic or trans-well filter

Project description:Transcriptome analyses reveal plasticity of phenotype with expression of principle and intercalated cell markers in this mouse kidney-derived cell line.

2022-07-18 | E-MTAB-11371 | biostudies-arrayexpress

scRNA-seq of pluripotent stem cell derived human intestinal organoids

Project description:Here, we used single cell RNA-sequencing (scRNA-seq) to profile pluripotent stem cell derived human intestinal organoids (HIOs) grown in matrigel or a non-adhesive alginate hydrogel after 28 days of in vitro growth. Additionally, we used scRNA-seq to profile HIOs derived in the presence of Neuregulin 1 (NRG1) and/or EGF after 40 days of in vitro growth.

2021-05-21 | E-MTAB-10268 | biostudies-arrayexpress

Single cell sequencing of renal endothelial cell heterogeneity and metabolic transcriptome adaptation to dehydration.

Project description:Renal endothelial cells (RECs) from glomerular cortical and medullary kidney compartments are exposed to different microenvironmental conditions. Upon dehydration medullary RECs (mRECs) are exposed to extreme hyperosmolarity. However the heterogeneous phenotypes of RECs remain in-completely inventoried and how mRECs respond to dehydration is unknown. By single cell RNA-sequencing of >40000 RECs we identified 24 (including 8 novel) REC phenotypes highlighting extensive heterogeneity of RECs between and within the cortex glomeruli and medulla. In response to dehydration mRECs upregulated primarily the expression of genes involved in the hypoxia response glycolysis and surprisingly oxidative phosphorylation (OXPHOS). In vitro mRECs increased oxygen consumption in response to hyperosmolarity presumably to sustain ATP production for Na+/K+ ATPase pump-mediated salt excretion and to generate metabolic water during OXPHOS in order to counteract mREC hyperosmolarity unveiling a previously underappreciated role of OXPHOS. Overall RECs exhibit extensive heterogeneity and plasticity to adapt their metabolic transcriptome to overcome dehydration.

2019-12-12 | E-MTAB-8145 | biostudies-arrayexpress

Single-cell RNA-seq of tumor-infiltrating lymphocytes in metastatic uveal melanoma

Project description:Metastatic uveal melanoma generally responds poorly to immunotherapy. The aim here was to sequence tumor-infiltrating lymphocytes from uveal melanoma metastases to study their phenotypes and T-cell receptor (TCR) clonotypes. We performed paired single-cell transcriptome and TCR sequencing using the 10x Genomics platform of IL2-expanded tumor-infiltrating lymphocytes from 7 liver and 1 subcutaneous metastasis.

2020-03-16 | E-MTAB-8846 | biostudies-arrayexpress

Comparative performance of the BGI and Illumina sequencing technology for single-cell RNA-sequencing

Project description:To compare the performance of Illumina and BGI sequencing technologies for high-throughput single cell sequencing, four Chromium single cell libraries of the following human cell types: Induced Pluripotent Stem Cells (hIPSC), cultured Trabecular MeshWork Cells (TMWC) and Peripheral Blood Mononuclear Cells (PBMCs), were sequenced on Illumina sequencers (NextSeq 500, NovaSeq 6000) and a BGI sequencer (MGISEQ-2000). The technologies were benchmarked based on sequencing quality, characterisation of cell populations within samples and for specific single cell analyses such as variant calling and detection of guide RNAs from pooled CRISPR screens.

2020-05-19 | E-MTAB-9024 | biostudies-arrayexpress

Single cell RNA sequencing of fetal mouse intestine at key stages of development (E13.5, E14.5, E15.5, E16 and E17.5)

Project description:Here, we present the fetal mouse intestine data from the project \\"Comparison of human and mouse mesenchyme identifies common and unique aspects of intestinal patterning\\". Whole intestines were harvested from fetuses from timed pregnant matings for wildtype C57BL/6 mice (Jax strain #000664). Fetal stages were confirmed according to the Theiler staging chart (https://www.emouseatlas.org/emap/ema/staging_criteria/staging_criteria.html). Whole intestines (from the common bile duct through the cecum) were collected at key stages of development (E13.5, E14.5, E15.5, E16 and E17.5). Male and female intestines from each stage were pooled and dissociated to single cells for single cell RNA sequencing as previously described (Miller et al. 2020 Dev Cell). Specifically, E13.5 was 6 intestines, E14.5 was 5 intestines, E15.5 was 4 intestines, E16 was 3 intestines and E17.5 was 3 intestines.

2024-04-01 | E-MTAB-13201 | biostudies-arrayexpress

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