Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing-based analysis of transcriptional reprogramming of primary human monocyte-derived macrophages infected with Mycobacterium tuberculosis

ABSTRACT: Primary human monocytes were isolated from four healthy human blood donors. Monocytes were isolated from PBMC buffy coats using plastic adherence for 4 hours. Monocytes were allowed to differentiate into macrophages over a period of 1 week. Macrophages from each of the 4 donors were split into two groups - uninfected and infected with Mycobacterium tuberculosis (Mtb). Cells in the infection group were infected with Mtb for 48 hours at a multiplicity of infection (MOI) of 10. Following incubation, uninfected and infected cells were harvested for RNA. RNA was used for next-generation RNA sequencing. Raw RNA sequencing data was processed using a HISAT2, Stringtie, Ballgown, DESeq2 pipeline. Processed data was used to measure differential expression between uninfected and infected macrophages.

ORGANISM(S): Homo sapiens

PROVIDER: GSE164287 | GEO | 2021/06/30

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Differential production of small RNAs in Mycobacterium tuberculosis infected primary human monocyte-derived macrophages

Project description:Primary human monocytes were isolated from four healthy donors. Monocytes were differentiated into macrophages, infected with virulent Mycobacterium tuberculosis (Mtb), strain H37Rv, for 24 or 48 hours, at a multiplicity of infection of 5 or 10. Following infection, infected cells and time-matched uninfected controls were harvested, total RNA including small RNAs was isolated and used for next-generation small RNA sequencing. Small RNA sequencing data was processed using miRge2.0, including a novel miRge2.0-based tRF detection tool. Processed data was used to determine differential expression of microRNAs and differential production of tRNA-derived fragments (tRFs) during infection with Mtb.

2020-10-15 | GSE151050 | GEO

Mycobacterium tuberculosis produces small noncoding RNAs that support mycobacterial survival in infected cells [miRNA discovery screen]

Project description:The purpose of this study was to identify Mtb- and hsa-encoded miRNAs produced in infected macrophages. RNA from 9 THP-1 samples (3 were uninfected, 3 were infected with Mtb H37Rv for 3 days and 3 were infected with Mtb H37Rv for 6 days) was sequenced and miRNAs were detected.

2020-02-24 | GSE145770 | GEO

Transcriptome analysis of primary human monocyte differentiation

Project description:In order investigate the control of genes encoding cytoskeletal motor proteins and their interaction partners in the activation program of primary monocytes, we performed whole transcriptome microarray profiling of ex vivo monocyte differentiation to activated macrophages or dendritic cells in monocytes isolated from three anonymous blood donors. Monocytes were isolated from the buffy coats of three anonymous blood donors and differentiated into activated macrophages or activated dendritic cells (DCs) ex vivo. Total RNA from monocytes, activated macrophages or DCs was isolated and submitted for whole transcriptome microarray analysis.

2013-01-23 | E-GEOD-33273 | biostudies-arrayexpress

Transcriptional effects of SARS-CoV-2 and their VLPs (virus-like particles) on human GM-CSF-derived macrophages

Project description:Analysis of the transcriptional signature of VLPs and SARS-CoV-2-infected human GM-CSF-dependent monocyte-derived macrophages. Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 1000 U/ml GM-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were exposed SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1), SARS-CoV-2-derived VLPs (MOCK) or nothing (UNT). After 4,12 and 36 hours, cells were lysed and RNA isolated for transcriptional analysis. We performed gene expression profiling analysis using data obtained from RNA-seq of 4 different donors.

2024-02-08 | GSE224845 | GEO

Methylglyoxal activates the NRF2 pathway and impairs immune responses controlling the growth control of Mycobacterium tuberculosis (Mtb) in macrophages.

Project description:We compared the transcriptome profile of M. tuberculosis-infected murine bone marrow derived macrophages (BMM) treated or not with 200 uM methylglyoxal (MGO) and uninfected controls as described below. We found 3606 differentially expressed genes (DEGs) between uninfected and M. tuberculosis-infected BMM, being approximately half of these upregulated . 1699 DEGs were determined by comparing Mtb-MGO vs M. tuberculosis BMM, with 2/3 of these DEGs downregulated. Genes in the glyoxalate, glutathione and selenocompound metabolic KEEG pathways were increased comparing Mtb-MGO vs M. tuberculosis BMM. Instead genes involved in type I IFN responses, cytokine receptor and chemokine signalling gene ontology clusters (GO) were increased after infection with Mtb as compared to uninfected controls and decreased in Mtb-MGO vs M. tuberculosis BMM.

2024-07-20 | GSE271061 | GEO

Single cell preparations of Mycobacterium tuberculosis damage the mycobacterial envelope and disrupt macrophage interactions

Project description:In order to investigate the impact of using in vitro techniques to generate single cell suspensions of Mycobacterium tuberculosis (Mtb) on macrophage gene expression, we compared uninfected bone marrow derived macrophages to macrophages infected with Mtb that was prepared using gentle sonication followed by low-speed centrifugation (so/sp) or passage through a 5 µm syringe filter (5µmF).

2022-06-23 | GSE206485 | GEO

Transcriptional effects of SARS-CoV-2 on human M-CSF-derived macrophages

Project description:Analysis of the transcriptional signature of SARS-CoV-2-infected human M-CSF-dependent monocyte-derived macrophages. Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes from three independent donors (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) at 37°C in a humidified atmosphere with 5% CO2 and 21% O2 for 7 days in the presence of 1000 U/ml M-CSF, with cytokine addition every two days. Then, monocyte-derived macrophages were exposed SARS-CoV-2 (SARS-CoV-2 clinical isolate Gisaid EPI_ISL_1120962, corresponding to ancestral S D614G, at an MOI=1) or nothing (UNT). After 4,12 and 36 hours, cells were lysed and RNA isolated for transcriptional analysis.

2023-12-24 | GSE207840 | GEO

Transcriptional effects of MAF- and MAFB-siRNAs on M-CSF-derived macrophages

Project description:Analysis of the role of transcriptions factors MAF and MAFB on the phenotypic profles of human M-CSF-derived macrophages. Methods: Human Peripheral Blood Mononuclear Cells (PBMC) were isolated from buffy coats from donors over a Lymphoprep gradient according to standard procedures. Monocytes were purified from PBMC by magnetic cell sorting using anti-CD14 microbeads (>95% CD14+ cells). Monocytes (0.5 x 106 cells/ml, >95% CD14+ cells) were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) for 7 days in the presence of 10 ng/ml M-CSF to generate M-CSF-polarized macrophages (M-MØ). Macrophages were differentiated from peripheral blood monocytes from 3 healthy donors with M-CSF (M-MØ) to generate anti-inflammatory M-MØ. Macrophages were transfected with either Control siRNA or MAFB-specific siRNA or MAF-specific siRNA for 24h and global gene expression was analysed by RNA-Seq.

2020-12-09 | GSE155719 | GEO

The sigma factor E of Mycobacterium tuberculosis modulates the inflammatory response of human THP1 cells

Project description:Mycobacterium tuberculosis (Mtb) is well adapted to survive in macrophages and usually subverts the bactericidal mechanisms of these professional phagocytes. The adaptation of Mtb to the intracellular life depends on its ability to regulate the expression of its genes. Among the most important bacterial transcription activators are the sigma factors that bind to the RNA polymerase and give it promotor specificity. Sigma factor E (SigE) controls the expression of genes that are essential for Mtb virulence. Analysis of the macrophage transcriptional response indicated that proteins encoded by the sigE regulon are involved in the modulation of the macrophage inflammatory response. We compared the global gene expression of THP1 macrophages infected with H37Rv and SigE to the gene expression profile of uninfected macrophages.

2010-05-25 | E-GEOD-7870 | biostudies-arrayexpress

The sigma factor E of Mycobacterium tuberculosis modulates the inflammatory response of macrophages

Project description:Mycobacterium tuberculosis (Mtb) is well adapted to survive in macrophages and usually subverts the bactericidal mechanisms of these professional phagocytes. The adaptation of Mtb to the intracellular life depends on its ability to regulate the expression of its genes. Among the most important bacterial transcription activators are the sigma factors that bind to the RNA polymerase and give it promotor specificity. Sigma factor E (SigE) controls the expression of genes that are essential for Mtb virulence. Analysis of the macrophage transcriptional response indicated that proteins encoded by the sigE regulon are involved in the modulation of the macrophage inflammatory response. We compared the global gene expression of mouse bone marrow macrofages infected with H37Rv and SigE to the gene expression profile of the uninfected macrophages.

2010-05-25 | E-GEOD-7871 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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