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Single-cell transcriptomic study of human paediatric tonsillar immune cells and sorted memory B cells using 10X Genomics: scVDJ-seq

ABSTRACT: Single-cell transcriptomic study of human paediatric tonsillar immune cells and sorted memory B cells using 10X Genomics: scVDJ-seq

PROVIDER: PRJEB38077 | ENA |

REPOSITORIES: ENA

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Single-cell transcriptomic study of human paediatric tonsillar immune cells and sorted memory B cells using 10X Genomics: scVDJ-seq

Project description:In response to antigen challenge, human B cells clonally expand, undergo selection and differentiate within secondary lymphoid tissues to produce mature B cell subsets and high affinity antibodies necessary for an effective immune response. However, the interplay between affinity, antibody class and different B cell fates has proved challenging to decipher in primary human tissue. We have applied an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics of human B cells from a model secondary lymphoid tissue. Specifically, here we have used single-cell sequencing of antibody repertoires using the 10X Genomics platform to profile unsorted immune cells and sorted memory B cells from paediatric tonsil tissue. Matched gene expression and bulk B cell repertoires are also available for the same patient donors.

2020-05-01 | E-MTAB-9003 | biostudies-arrayexpress

Single-cell transcriptomic study of human paediatric tonsillar immune cells and sorted memory B cells using 10X Genomics: scRNA-seq

Project description:In response to antigen challenge, human B cells clonally expand, undergo selection and differentiate within secondary lymphoid tissues to produce mature B cell subsets and high affinity antibodies necessary for an effective immune response. However, the interplay between affinity, antibody class and different B cell fates has proved challenging to decipher in primary human tissue. We have applied an integrated analysis of bulk and single-cell antibody repertoires paired with single-cell transcriptomics of human B cells from a model secondary lymphoid tissue. Specifically, here we have used single-cell RNA-seq using the 10X Genomics platform to profile unsorted immune cells and sorted memory B cells from paediatric tonsil tissue. Matched single-cell VDJ data and bulk B cell repertoires are also available for the same patient donors.

2020-05-01 | E-MTAB-9005 | biostudies-arrayexpress

Single-cell transcriptomic study of human paediatric tonsillar immune cells and sorted memory B cells using 10X Genomics: scRNA-seq

Project description:Single-cell transcriptomic study of human paediatric tonsillar immune cells and sorted memory B cells using 10X Genomics: scRNA-seq

| PRJEB38087 | ENA

lung and tonsillar mast cells

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2004-10-20 | GSE1848 | GEO

CMV-CTLs scVDJ-RNAseq

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Transcription profiling of human lung and tonsillar mast cells

Project description:GeneChip Data of human lung mast cells and tonsillar mast cells

2008-06-11 | E-GEOD-1848 | biostudies-arrayexpress

Gene expression profiles of normal human tonsillar cell subpopulations FACS sorted based on expression of cell surface markers

Project description:To characterize the progenitor-enriched CD44+NGFR+ cells present in the crypt and surface regions of the tonsil, we used an Illumina array system to analyze the transcriptome of these cells isolated from the tonsillar crypt and surface regions of three different individuals as well as the total epithelial (CD45-CD31-) populations obtained from two of these.

2015-10-29 | GSE69767 | GEO

Distinct stage-specific transcriptional states of B cells in human tonsillar tissue [single-cell RNA-seq]

Project description:Defining B cell states in human tonsillar tissue using single cell transcriptomics.

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Transcriptomic analysis of differential expressed genes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection

Project description:Purpose: The goals of this study are to understand the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection and determine the differential expressed genes Methods: Transcriptional profiles of human tonsillar epithelial cells UT-SCC-60B and human tonsillar epithelial cells infected with EV71 were generated by next generation sequencing, in triplicate, using Illumina X-ten/NovaSeq. The sequence reads that passed quality filters were analyzed abundance of mRNA using StringTie, the FPKM values of genes and transcripts were calculated by Ballgown of R software, alternative splicing events were determined by rMATS Results: Using an optimized data analysis workflow, we mapped more than 36 million sequence reads per sample. Total 11137 gene counts and 26860 transcript counts were identified in human tonsillar epithelial cells, 11347 gene counts and 27994 transcript counts were identified in EV71-infected human tonsillar epithelial cells. Total 96 genes and 499 transcripts were down-regulated, 105 genes and 550 transcripts were up-regulated according the criteria that fold changes are more than 1.5, p value less is than 0.05 and mean of FPKM value is more than 0.5 to defined as the differential expressed genes or differential expressed transcripts. Total 11563 novel genes and 14927 novel transcripts were identified and 3266 novel transcripts had the potential coding probabilities. Finally, total 5742 genes occurred alternative splicing events. Conclusions: Our study represents the first detailed analysis of the transcriptional changes of human tonsillar epithelial cells UT-SCC-60B in response to EV71 infection, this results will provide novel insight into the interaction between human tonsillar epithelial cells and EV71

2019-08-31 | GSE136668 | GEO

Purified intestinal epithelial cells from foetal and paediatric gut

Project description:CD326+ sorted intestinal epithelial cells from foetal (9-12 wk gestational age) small bowel and large bowel, CD326+ sorted intestinal epithelial cells from mucosal biopsies of paediatric (5-15 years of age) terminal illeum, ascending colon and sigmoid colon FPG=Foetal proximal gut, FDG=Foetal distal gut, PTI=paediatric terminal ileum, PAC=paedaitric ascending colon, PSC=paediatric sigmoid colon

2015-09-15 | E-MTAB-3704 | biostudies-arrayexpress

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