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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [BMDM]

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [BMDM]

PROVIDER: PRJNA623344 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11486700_1.fastq.gz	Fastqsanger.gz
	SRR11486700_2.fastq.gz	Fastqsanger.gz
	SRR11486701_1.fastq.gz	Fastqsanger.gz
	SRR11486701_2.fastq.gz	Fastqsanger.gz
	SRR11486702_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [BMDM]

Project description:We used RNA-seq to detect the genes affectded by Tet2 or Itaconate (ITA) treatment

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [RAW264.7]

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [RAW264.7]

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Tet2 Mutant Macrophage Transcriptomes [RAW264.7]

Project description:We used RNA-seq to detect the genes affected by Tet2 or Itaconate (ITA) treatment

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Cd226-/- BMDM Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare WT-BMDM vs. cd226-BMDM transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

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Expression data from pig BMDM treated with salmonella LPS

Project description:Mouse bone marrow-derived macrophages (BMDM) grown in macrophage colony-stimulating factor (CSF-1) have been used widely in studies of macrophage biology and the response to toll-like receptor agonists. We investigated whether similar cells could be derived from the domestic pig. Cultivation of pig bone marrow cells for 5-7 days in presence of rhCSF-1 generated a pure population of BMDM that expressed the usual macrophage markers (CD14, CD16, CD163, CD172a), are potent phagocytic cells and produced tumor necrosis factor (TNF) in response to lipopolysaccharide (LPS). Bone marrow cells could be stored frozen and thawed, providing a renewable resource. We profiled gene expression in pig BMDM from outbred animals (Large-White Landrace F1cross) responding to LPS using Affymetrix microarrays. The temporal cascade of inducible and repressible genes more closely-resembled human than mouse macrophages, and included genes involved in tryptophan metabolism (IDO, KYN), lymphoattractant chemokines (CCL20) and the vitamin D3-converting enzyme Cyp27B1. Conversely, pig BMDM, like human macrophages, did not induce genes involved in arginine metabolism, nor did they produce nitric oxide. The data establish pig BMDM as an alternative tractable model for the study of macrophage transcriptional control. RNA for gene expression analysis was collected at time points 0, 2, 7 and 24 hours post LPS stimulation (100ng/ml). Each time point included BMDM from the same three pigs and each cell culture was replicated. The replicate of the pig3_24h was not suitable for RNA analysis. Therefore, a total of 23 microarrays were hybridized.

2011-08-31 | E-GEOD-30956 | biostudies-arrayexpress

Downstream Molecules of YKL-40 in Regulating Apoptosis in BMDM

Project description:An iTRAQ-based proteomics analysis was performed on BMDM to screen out the potential downstream target molecules of YKL-40 in regulating macrophage apoptosis.

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Tet2 facilitates the de-repression of myeloid target genes during C/EBPa induced transdifferentiation of pre-B cells

Project description:Tet2 is an enzyme that hydroxylates methylated cytosines and has been implicated in hematopoietic differentiation and the formation of myeloid malignancies when mutated. An ideal system to study the role of Tet2 in myelopoeisis is C/EBPa induced transdifferentiation of pre-B cells into macrophages, where many myeloid genes become rapidly upregulated. Here we found that C/EBPa binds to upstream regions of Tet2 and that the gene becomes activated. Tet2 knockdowns impaired the upregulation of macrophage markers as well as phagocytic capacity, suggesting that the enzyme is required for both early and late stages of myeloid differentiation. A slightly weaker effect was seen in primary cells with a Tet2 ablation. Expression arrays of transdifferentiating cells with Tet2 knockdowns permitted the identification of a small subset of myeloid genes whose upregulation was blunted. Activation of these target genes was accompanied by a rapid increase of promoter hydroxy-methylation. Our observations indicate that Tet2 helps C/EBPa to rapidly de-repress myeloid genes during the conversion of pre-B cells into macrophages. Gene expression was measured in a control and Tet2kd mouse preB cell line (called Haftl) harboring an inducible form of C/EBPa. Expression was measured in starting cells and cells induced to transdifferentiate into macrophage-like cells for 24 hours. Technical duplicates for each treatment and time were assayed.

2012-07-26 | E-GEOD-39666 | biostudies-arrayexpress

OGT, H2B S112GlcNAc, TET2 ChIP-seq results

Project description:TET2 directly interacts with OGT, which is important for the chromatin association of OGT in vivo. Although this specific interaction does not regulate the enzymatic activity of TET2, it facilitates OGT-dependent histone O-GlcNAcylation. Moreover, OGT associates with TET2 at transcription starting sites (TSS). Down-regulation of TET2 reduces the amount of H2B S112 GlcNAc marks in vivo, which are associated with gene transcription regulation. We found that OGT interacts with TET2 tightly. Using ChIP-seq with specific antibodies, we tested the co-localization of TET2 and OGT in genome level.

2012-12-11 | E-GEOD-41720 | biostudies-arrayexpress

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