Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Homo sapiens

SUBMITTER: Mangesh Bhide

PROVIDER: E-MTAB-8008 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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 Borrelia garini .

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

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

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

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

2021-01-01 | E-MTAB-9755 | 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

RNA-seq of human neutrophil-like cell line PLB-985 at various stages of differentiation with CRISPR knock-outs of H1 linker histones

Project description:Finding that PLB-985 knockouts of H1.2 or H1.4 were deficient in their differentiation to neutrophil-like cells, we decided to perform RNA-seq on 2 single-cell clones of knockouts of each of the linker histones H1.1-H1.5.

2020-05-11 | E-MTAB-8459 | biostudies-arrayexpress

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

Genome-wide transcriptome comparison between primary cultures of human dermal microvascular endothelial cells and infantile hemangioma endothelial cells

Project description:Whole transcriptome comparisons of proliferating pure cultures of neonatal dermal microvacsular endothelial cells to infantile hemangioma endothelial cells. The total RNA was obtained from human dermal microvascular endothelial cells and infantile hemangioma endothelial cells. Illumina microarrays were performed to determine the whole genome expression differences between the cell lines.

2013-06-01 | E-GEOD-43742 | 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