Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Profiling of the brain endothelial transcriptional changes upon Gpr126 depletion at P18

ABSTRACT: RNA-seq experiment of WT and Gpr126iECKO mice with Gpr126 depletion at P18. Two replicates per condition.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Mus musculus

SUBMITTER: Data Submission IFOM ETS

PROVIDER: E-MTAB-13914 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq comparison of fibro-adipogenic progenitors (FAPs) from wild type, mdx and cardiotoxin-injured mice

Project description:We purified FAPs from the hind limbs of wild type, mdx and cardiotoxin-injured mice in order to unveil changes in their transcriptomes. RNA was isolated directly from sorted cells and analyzed by 3’ RNA sequencing.

2019-06-20 | E-MTAB-8040 | 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

A single cell transcriptome atlas of murine endothelial cells

Project description:The heterogeneity of endothelial cells (ECs), lining blood vessels, across tissues remains incompletely inventoried. We constructed an atlas of >32,000 single-EC transcriptomic data from 11 tissues of the model organism Mus musculus. We propose a new classification of EC phenotypes based on transcriptome signatures and inferred putative biological features. We identified top-ranking markers for ECs from each tissue. ECs from different vascular beds (arteries, capillaries, veins, lymphatics) resembled each other across tissues, but only arterial, venous and lymphatic (not capillary) ECs shared markers, illustrating a greater heterogeneity of capillary ECs. We identified high-endothelial-venule and lacteal-like ECs in the intestines, and angiogenic ECs in healthy tissues. Metabolic transcriptomes of ECs differed amongst spleen, lung, liver, brain and testis, while being similar for kidney, heart, muscle and intestines. Within tissues, metabolic gene expression was heterogeneous amongst ECs from different vascular beds, altogether highlighting large EC heterogeneity.

2020-02-13 | E-MTAB-8077 | biostudies-arrayexpress

Mitochondrial perturbation in the intestine causes microbiota-dependent injury and gene signatures discriminative of inflammatory disease

Project description:Single-cell RNA-sequencing (scRNA-seq) data was generated from colonic tissue from Hsp60Δ/ΔIEC and Hsp60fl/fl mice at day 8 enriched in intestinal epithelial cells (IECs).

2024-07-10 | E-MTAB-14206 | biostudies-arrayexpress

LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from 3-, 6-, 12-, and 18-months-old mice and Apoe-KO mice at 3 months followed by label-free quantification (LFQ)

Project description:Age-related decline in brain endothelial cell (BEC) function critically contributes to cerebrovascular and neurodegenerative disease. Comprehensive atlases of the BEC transcriptome have become available but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting (MACS)-based mouse BEC enrichment protocol compatible with high-resolution mass-spectrometry based proteomics. In this experiment, first we have compared MACS sorted BECs across multiple time points between 3 and 18 months of age. Using unsupervised cluster analysis, we found a segregation of age-related protein dynamics with biological functions including a downregulation of vesicle-mediated transport. Our approach uncovered changes not picked up by transcriptomic studies such as accumulation of vesicle cargo and receptor ligands including Apoe. Therefor in our next proteomics experiment we compared BECs from 3-months-old Apoe-KO and WT mice and found 111 and 103 proteins to be up- and downregulated, respectively. Comparing the BEC proteomic signature of young Apoe-KO mice with the signature of aged (18-months-old) WT mice we found a positive correlation suggesting an accelerating effect of Apoe deficiency on BEC aging.

2024-02-15 | PXD044996 | Pride

LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from ARF6-KO and WT mice followed by label-free quantification (LFQ)

Project description:Age-related decline in brain endothelial cell (BEC) function critically contributes to cerebrovascular and neurodegenerative disease. Comprehensive atlases of the BEC transcriptome have become available but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting (MACS)-based mouse BEC enrichment protocol compatible with high-resolution mass-spectrometry and analysed the profiles of protein abundance changes across multiple time points between 3 and 18 months of age and identified Arf6 as one of the most prominently downregulated vesicle-mediated transport protein during BEC aging. To better understand the role of Arf6 in BECs, in this experiment we have compared MACS sorted BECs from Arf6-KO and WT 3-months-old mice and found 140 and 172 proteins to be significantly down- and upregulated, respectively. Enrichment analyses of significantly downregulated proteins showed mRNA processing to be among the most affected biological processes consistent with our findings on the aged BEC proteome.

2024-02-15 | PXD045004 | Pride

LC-MS/MS analysis of isolated murine brain endothelial cells (BECs) from Arf6-GFP-AAV vs GFP-AAV treated WT mice followed by label-free quantification (LFQ)

Project description:Age-related decline in brain endothelial cell (BEC) function critically contributes to cerebrovascular and neurodegenerative disease. Comprehensive atlases of the BEC transcriptome have become available but results from proteomic profiling are lacking. To gain insights into endothelial pathways affected by aging, we developed a magnetic-activated cell sorting (MACS)-based mouse BEC enrichment protocol compatible with high-resolution mass-spectrometry and analysed the profiles of protein abundance changes across multiple time points between 3 and 18 months of age and identified Arf6 as one of the most prominently downregulated vesicle-mediated transport protein during BEC aging. To better understand the role of Arf6 in BECs, in this experiment we have compared MACS sorted BECs from Arf6-GFP-AAV vs GFP-AAV treated 3-months-old WT mice and found 86 and 110 proteins to be significantly down- and upregulated, respectively. Enrichment analyses of significantly upregulated proteins revealed vesicle-mediated transport, activation of GTPase activity, and ER to Golgi vesicle-mediated transport to be among the most significantly affected biological processes.

2024-02-15 | PXD045006 | Pride

Single-cell RNAseq of human bone marrow cells enriched for stromal and endothelial markers

Project description:Gene expression profiles of individual bone marrow cells were acquired by Drop-Seq. Subsets of bone marrow cells were isolated using magnetic cell sorting to enrich for putative skeletal stem cells.

2021-06-30 | E-MTAB-9662 | biostudies-arrayexpress

scRNA seq analysis of CD45+ tumor infiltrating cells (TICs) of B16F10 tumor-bearing Trem1+/+ and Trem1-/- mice.

Project description:To gain a global understanding of the impact of TREM1 silencing, we analyzed the CD45+ tumor infiltrating cells (TICs) of B16F10 tumor-bearing Trem1+/+ and Trem1-/- mice. Utilizing the 10x Genomics Chromium Platform, we analyzed approximately 5390 cells per sample with a coverage rate of 15493 genes per cell.

2023-09-27 | E-MTAB-13237 | biostudies-arrayexpress

3'end RNA sequencing of TDP-43 depleted and mutant TDP-43-rescued Hek-293 FlpIn lines

Project description:This project studies TDP43, which is an RNA binding protein implicated in Motor Neuron Disease. As an RNA-binding protein, TDP43 is known to influences poly-adenylation site choice. For this project, we have inserted a single copy of the GFP-tagged TDP43 gene into the FLPIn Locus of HEk293 cells. We use these Hek293 FLipIn lines to instigate the effect of different deletion and mutation constructs of TDP-43 in their ability to rescue the depletion (siRNA) of the endogenous TDP-43 protein. We are comparing siRNA mediated KD in triplicates for each of the 7 cell lines to the Dox-induced rescues in triplicates. We are using a customised Lexogen Quantseq 3’ end sequencing method that allows us to multiplex cDNAs straight after the reverse transcription. The samples were pooled into barcoded sub-groups, each group will have the Lexogen barcode (i7 indices) in addition.

2021-07-21 | E-MTAB-9410 | 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