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Assay for Transposase-Accessible Chromatin using sequencing of PD-1+ Tfh cells and CD62L+ Tfh cells

ABSTRACT: Assay for Transposase-Accessible Chromatin using sequencing of PD-1+ Tfh cells and CD62L+ Tfh cells

PROVIDER: PRJNA961133 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24287976_1.fastq.gz	Fastqsanger.gz
	SRR24287976_2.fastq.gz	Fastqsanger.gz
	SRR24287977_1.fastq.gz	Fastqsanger.gz
	SRR24287977_2.fastq.gz	Fastqsanger.gz

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Assay for Transposase-Accessible Chromatin using sequencing of PD-1+ Tfh cells and CD62L+ Tfh cells

Project description:T follicular helper (Tfh) cells, essential for germinal center reactions, are not identical, with different phenotypes reported. Whether, when and how they generate memory cells are still poorly understood. Here, through single-cell RNA-sequencing analysis of CXCR5+Bcl6+ Tfh cells generated under different conditions, we discovered, in addition to PD-1hi effector Tfh cells, a CD62L+PD1low subpopulation. CD62L-expressing Tfh cells developed independently from PD-1+ cells, and not in direct contact with B cells. More importantly, CD62L+ Tfh cells expressed memory- and stemness-associated genes; with more superior long-term survival, they readily generated PD-1hi cells in the recall response. Finally, KLF2 and IL7R, also highly expressed by CD62L+ Tfh cells, were required to regulate their development. Our work thus demonstrates a novel Tfh memory-like cell subpopulation, which may benefit our understanding on immune responses and diseases.

2023-11-17 | GSE230437 | GEO

Global gene expression profile of PD1+ Tfh cells, CD62L+ Tfh cells, non-Tfh effector cells

2023-11-17 | GSE230436 | GEO

Global gene expression profile of PD1+ Tfh cells, CD62L+ Tfh cells, non-Tfh effector cells

Project description:Global gene expression profile of PD1+ Tfh cells, CD62L+ Tfh cells, non-Tfh effector cells

| PRJNA961134 | ENA

Assay for Transposase-Accessible Chromatin in E4BP4 overexpressed RAW264.7 cells

Project description:Assay for Transposase-Accessible Chromatin in E4BP4 overexpressed RAW264.7 cells

| PRJNA978597 | ENA

Assay for Transposase-Accessible Chromatin using sequencing of spleen memory CD4+ T cells

Project description:Assay for Transposase-Accessible Chromatin using sequencing of spleen memory CD4+ T cells

| PRJNA579595 | ENA

Single cell RNA-sequencing of Tfh cells and Tfr cells

2023-11-16 | GSE230435 | GEO

Assay for Transposase Accessible Chromatin (ATAC)-sequencing of the AML cell line U937

Project description:Assay for Transposase Accessible Chromatin (ATAC)-sequencing of the AML cell line U937

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Assay for transposase-accessible chromatin with sequencing (ATAC-seq) after various treatments in T47D cells

Project description:Assay for transposase-accessible chromatin with sequencing (ATAC-seq) after various treatments in T47D cells

| PRJNA1055469 | ENA

Chromatin changes in lateral organ founder cells of Arabidopsis thaliana detected by assay for transposase-accessible chromatin sequencing (ATAC-seq)

Project description:Two methods Fluorescence Activated Cell Sorting (FACS) and Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) are combined to analyse the chromatin accessibility of Lateral Organ Founder Cells (LOFCs) in the peripheral zone of the apetala1 cauliflower double mutant Arabidopsis inflorescence meristem. Genome-wide we observed a striking correlation between Transposase Hypersensitive Sites (THS) detected in ATAC-seq and DNase I Hypersensitive Sites (DHS), covering mostly extended regions substructured into several individual THS that correspond to phylogenetically conserved sequence, enhancer elements and binding sites of MADS-box transcription factors. Relative to available RNA-seq data, chromatin configuration changes according to gene activation or repression, i.e. at cellular resolution chromatin regions gain or lose Tn5 transposase accessibility in direct correlation with gene expression levels. A pronounced THS priority immediately upstream of the transcription start and reduced numbers of THSs in the transcription unit are complementary to established H3K4me3 activation or H3K27me3 repressive marks. At this resolution, the FACS/ATAC-seq combination should be widely applicable to detect chromatin changes in course of cell type specification and facilitate the detection of regulatory promoter elements in plant promoters.

2019-04-02 | GSE116972 | GEO

Optimized protocol for assay for transposase-accessible chromatin by sequencing (ATAC-seq) from Drosophila melanogaster brain tissue

Project description:Transposase-accessible chromatin by sequencing (ATAC-seq) has emerged as an advantageous technique to assess chromatin accessibility owing to the robustness of "tagmentation" process and a relatively faster library preparation. A comprehensive ATAC-seq protocol from Drosophila brain tissue is currently unavailable. Here, we have provided a detailed protocol of ATAC-seq assay from Drosophila brain tissue. Starting from dissection and transposition to amplification of libraries has been elaborated. Furthermore, a robust ATAC-seq analysis pipeline has been presented. The protocol can be easily adapted for other soft tissues.

2023-10-24 | GSE246106 | GEO

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