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

Transcriptome analysis of 3D model of blood-brain barrier exposed to tick-borne encephalitis virus (TBEV)

ABSTRACT: Using RNA sequencing to map differentially expressed genes in the 3D model of the blood-brain barrier ( composed of human brain endothelial cells, human astrocytes, and human pericytes) challenged with TBEV.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Mangesh Bhide

PROVIDER: E-MTAB-9755 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcriptome analysis of 3D model of blood-brain barrier exposed to West Nile virus (WNV)

Project description:Using RNA sequencing to map differentially expressed genes in the 3D model of the blood-brain barrier ( composed of human brain endothelial cells, human astrocytes, and human pericytes) challenged with WNV.

2021-01-01 | E-MTAB-9754 | biostudies-arrayexpress

Transcriptome analysis of 3D model of blood-brain barrier exposed to Borrelia garini

2021-01-01 | E-MTAB-9753 | biostudies-arrayexpress

Transcriptome analysis of human brain microvascular endothelial cells response to Borrelia burgdorferi and its antigen Erp23 using RNA-seq

Project description:Using RNA sequencing to map differentially expressed genes in human brain microvascular endothelial cells challenged with Borrelia burgdorferi or its ligand Erp23.

2019-06-21 | E-MTAB-8053 | biostudies-arrayexpress

Transcriptome analysis of human brain microvascular endothelial cells response to interactive DIII domain of protein E of WNV and interactive DIII domain of protein E of TBEV using RNA-seq

Project description:Using RNA sequencing to map differentially expressed genes in human brain microvascular endothelial cells challenged with DIII domain of protein E of WNV and DIII domain of protein E of TBEV.

2019-06-22 | E-MTAB-8052 | biostudies-arrayexpress

Transcriptome analysis of human brain microvascular endothelial cells response to Streptococcus pneumoniae and its antigen Adhesion lipoprotein using RNA-seq

Project description:Using RNA sequencing to map differentially expressed genes in human brain microvascular endothelial cells challenged with Streptococcus pneumoniae or its ligand Adhesion lipoprotein.

2019-06-22 | E-MTAB-8054 | biostudies-arrayexpress

Transcriptome analysis of human brain microvascular endothelial cells response to Neisseria meningitidis and its antigen MafA using RNA-seq

Project description:Using RNA sequencing to map differentially expressed genes in human brain microvascular endothelial cells challenged with Neisseria meningitidis or its ligand MafA .

2019-06-15 | E-MTAB-8008 | biostudies-arrayexpress

Combinatorial treatment with PARP and MAPK inhibitors to overcome phenotype switch-driven drug resistance in advanced melanoma

Project description:Metastatic melanoma is either intrinsically resistant or rapidly acquires resistance to targeted drugs such as MAPK inhibitors (MAPKi). Here, using a drug screen targeting chromatin regulators in patient-derived 3D melanoma cell cultures, we discovered that PARP inhibitors are capable of restoring MAPKi sensitivity. This synergy was found to be independent of DNA damage repair pathways and was effective both in vitro and in vivo in patients-derived xenografts. Strikingly, through integrated transcriptomic, proteomic and epigenomic analysis, we discovered that PARPi induces lysosomal autophagy which was accompanied by enhanced mitochondrial lipid metabolism that, ultimately, increased antigen presentation and sensitivity to T-cell cytotoxicity. Moreover, we also found that PARP inhibitors regulated EMT-like phenotype switching by dampening the mesenchymal phenotype via transcriptomic and epigenetic rearrangements. This, in turn, redirected melanoma cells towards a proliferative and, thus, MAPKi-sensitive state. Our study provides a scientific rational for treating patients with PARPi in combination with MAPKi to annihilate acquired therapy resistance.

2023-09-08 | PXD038822 | Pride

Transcriptomic profiling of human neuromesodermal-like cells and spinal cord progenitors derived in vitro from H9 ES cell line

Project description:Human ES (H9) cells were directed towards a neuromesodermal progenitor-like cell state and these cells were then subsequently differentiated towards a neural cell fate. Human ES cells (H9) were differentiated into neuromesodermal progenitor-like cells by culturing in Neurobasal/1x N2/1x B27 medium (N2/B27) supplemented with 20 ng/ml bFgf and 3 μM CHIR99021 for 3 days and exposure to dual SMAD inhibition (dSMADi) (Noggin 50 ng/ml and the TGFb receptor type 1 inhibitor SB431542 10 μM) during day 3 (D3). Transcriptome analysis was then carried out following a selection procedure to enrich for NMP-like cells (sD3/NMP-like). This involved use of a hES (H9) cell line engineered with CRISPR-Cas9 to express GFP under the control of the endogenous Nkx1.2 promoter. At the end of day 3 cells were selected for high GFP expression, as high Nkx1.2 transcription is characteristic of NMP cell populations in mouse and chick embryos. These cells were then lysed and RNA extracted for RNASeq. Humans ES cells (H9) differentiated into NMP-like cells as above (without selection) were also allowed to develop further on day 4 (in the presence of dSMADi and Retinoic acid (RA) 100nM, in N2/B27) and then in RA alone until end of day 8 (D8). These cells were then lysed and RNA extracted for RNASeq.

2018-07-04 | E-MTAB-6680 | biostudies-arrayexpress

RNA sequencing of blood brain barrier spheroids exposed to either Neisseria meningitidis or Borrelia bavariensis in in vitro conditions

Project description:Neisseria meningitidis and Borrelia bavariensis are the causative agents of invasive meningococcal disease and Lyme neuroborrelosis. Before infecting the brain parenchyma the bacterial pathogens should cross the human blood-brain barrier (BBB). To understand the response of BBB against the invading pathogens, in vitro BBB spheroid model was generated by co cultivating human brain microvascular endothelial cells, pericytes and astrocytes in low adhesion conditions. Spheroids (N= 36) were infected with either N. meningitidis (6 x 10e4, MOI 1:4) or B bavariensis(1.5 x 10e5, MOI 1:10) for 3h. Two separate control groups of spheroids (N=36) without any infection were included in the study. After 3h of treatment (infection/no infection), 12 spheroids were pooled to form one biological sample and such 3 biological replicates per treatment were sampled for total RNA extraction. Thereafter, 12 cDNA libraries were prepared using QuantSeq FWD 3’mRNA Library Prep Kit (Lexogen). Second strand of cDNA library was synthesized using the UMI Second Strand Synthesis Mix (USS, Lexogen) containing 6 nucleotides long Unique Molecular Identifiers (UMIs). The double stranded cDNA libraries were amplified in 17-19 PCR cycles using i5 Unique Dual Indexing Add-on Kit (Lexogen). Illumina NextSeq 500 was employed to sequence the libraries having a read lengths of single-end 75 bp producing about 10 million reads per library. To carryout gene expression analysis, Bioconductor R-package - DESeq2 v1.20.0 (Love et al., 2014) was used where in, featureCounts tool v1.6.3 (Liao et al., 2013) was used to enumerate the genes. A minimum threshold of adjusted p-value < 0.05 and log2fold-change (log2FC) = ± 1 was set to considered the gene as differentially expressed (DEG).

2023-10-31 | E-MTAB-13401 | biostudies-arrayexpress

Kidney spheroids generate a functional quiescent niche leading to enhanced tubulogenic potency of human kidney-derived cells

Project description:Cell-based approaches utilizing autologous human renal cells require their isolation, expansion in vitro and reintroduction back into the host for renal tissue regeneration. Nevertheless, human kidney epithelial cells (hKEpC) lose their phenotype, dedifferentiate and assume the appearance of fibroblasts after relatively few passages in culture. We hypothesized that growth conditions may influence hKEpC phenotype and function. hKEpC retrieved from human nephrectomy tissue samples showed the ability to reproducibly form kidney-spheres when grown in suspension culture developed in non-adherent conditions. Genetic labeling and time-lapse microscopy indicated, at least in part, the aggregation of hKEpC into 3D-spheroids rather than formation of pure clonally expanded spheres. Characterization of hKEpC spheroids by real-time PCR and FACS analysis showed up-regulation of some renal developmental and 'stemness' markers compared to monolayer and mostly an EpCAM+CD24+CD133+CD44+ spheroid cell phenotype. Oligonucleotide microarrays which were used to identify global transcriptional changes accompanying spheroid formation, showed predominantly up-regulation of cell matrix/cell contact molecules and cellular biogenesis processes and down-regulation of cell cycle, growth and locomotion. Accordingly, hKEpC spheroids proliferated slowly as indicated by low Ki-67 staining, but when grafted in low cell numbers onto the chorioallantoic membrane (CAM) of the chick embryo, they exclusively reconstituted various renal tubular epithelia. Moreover, efficient generation of kidney spheroids was observed after long-term monolayer culture resulting in re-establishment of tubulogenic capacity upon CAM grafting. Thus, generation of a specialized quiescent niche in hKEpC spheroids may provide a functional benefit for kidney-derived cells in vivo. 6 samples, 3 adherent and 3 spheroids samples

2011-12-31 | E-GEOD-28052 | 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