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Transcriptional analysis of dendritic cells upon TLR stimulation reveals an immunosuppressive profile [cut&tag]

ABSTRACT: Transcriptional analysis of dendritic cells upon TLR stimulation reveals an immunosuppressive profile [cut&tag]

PROVIDER: PRJNA1083872 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28227817_1.fastq.gz	Fastqsanger.gz
	SRR28227817_2.fastq.gz	Fastqsanger.gz
	SRR28227818_1.fastq.gz	Fastqsanger.gz
	SRR28227818_2.fastq.gz	Fastqsanger.gz
	SRR28227819_1.fastq.gz	Fastqsanger.gz

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KLF5 CUT&Tag of HBECs at ALI with and without IL-13 stimulation

Project description:Using CUT&Tag, we examined KLF5-associated genomic regions in primary human bronchial epithelial cells (HBECs) cultured at air-liquid interface (ALI) with and without IL-13 stimulation.

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Transcriptional analysis of dendritic cells upon TLR stimulation reveals an immunosuppressive profile [cut&tag]

Project description:Dendritic cells (DCs) simultaneously prime and dampen the immune response. The transcriptional program that regulates immunosuppression in DCs is currently unknown. Here we identified ETS homologous factor as a key transcription factor that regulates DC immunosuppression.

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HCT116_SMARCA4 CUT&Tag

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Effect of TLR Ligation on the Differentiation and Function of Human mMDSC

Project description:Immunosuppressive microenvironments block the activity of tumoricidal T and NK cells, allowing cancers to avoid immune elimination. Monocytic myeloid-derived suppressor cells (mMDSC) are an important component of these immunosuppressive milieus. Human mMDSC respond to stimulation via their Toll-like receptors by differentiating into macrophage. Agonists targeting TLRs 1/2 (such as PAM3) induce mMDSC to mature into immumosuppressive M2-like macrophage through a process that involves TNF and IL6. Agonists targeting TLRs 7/8 (such as R848) cause the same precursors to mature into tumoricidal M1-like macrophages, a process in which IL12 plays a central role. The immune suppression mediated by mMDSC is reversed by exposure to TLR 7/8 agonists which thus might be useful adjuncts for tumor immunotherapy. In this study we looked at several time points. hMDSC from four different donors were sorted from PBMC then cultured in the presence of R848, Pam 3 or left unstimulated for 30, 75 and 225 minutes. Late time points included samples from seven donors after 3 days in culture with the same TLR ligands. For microarray experiments total RNA was extracted, amplified into aRNA and coupled to Cy5. Similarly amplified RNA from universal RNA was coupled to Cy3 and used as a reference for each array.

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Project description:We developed scNanoSeq-CUT&Tag, a streamlined method by adapting a modified CUT&Tag protocol to Oxford Nanopore sequencing platform for efficient chromatin modification profiling at single-cell resolution. We firstly tested the performance of scNanoSeq-CUT&Tag on six human cell lines: K562, 293T, GM12878, HG002, H9, HFF1 and adult mouse blood cells, it showed that scNanoSeq-CUT&Tag can accurately distinguish different cell types in vitro and in vivo. Moreover, scNanoSeq-CUT&Tag enables to effectively map the allele-specific epigenomic modifications in the human genome andallows to analyze co-occupancy of histone modifications. Taking advantage of long-read sequencing,scNanoSeq-CUT&Tag can sensitively detect epigenomic state of repetitive elements. In addition, by applying scNanoSeq-CUT&Tag to testicular cells of adult mouse B6D2F1, we demonstrated that scNanoSeq-CUT&Tag maps dynamic epigenetic state changes during mouse spermatogenesis. Finally, we exploited the epigenetic changes of human leukemia cell line K562 during DNA demethylation, it showed that NanoSeq-CUT&Tag can capture H3K27ac signals changes along DNA demethylation. Overall, we prove that scNanoSeq-CUT&Tag is a valuable tool for efficiently probing chromatin state changes within individual cells.

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