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RNA-sequencing of pre-GC B cells helped by CD4-CrexBcl6fl/+ or CD4-Cre OT-II T cells

ABSTRACT: RNA-sequencing of pre-GC B cells helped by CD4-CrexBcl6fl/+ or CD4-Cre OT-II T cells

PROVIDER: PRJNA749751 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR15249649_1.fastq.gz	Fastqsanger.gz
	SRR15249649_2.fastq.gz	Fastqsanger.gz
	SRR15249650_1.fastq.gz	Fastqsanger.gz
	SRR15249650_2.fastq.gz	Fastqsanger.gz
	SRR15249651_1.fastq.gz	Fastqsanger.gz

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RNA-sequencing of pre-GC B cells helped by CD4-CrexBcl6fl/+ or CD4-Cre OT-II T cells

Project description:We analyzed transcriptome differences of antigen-specific pre-GC B cells. We transferred wildtype (CD4-Cre) or BCL6-insufficient (CD4-CrexBcl6fl/+) OT-II T cells into SAP-deficient mice and immunized these mice with NP-OVA. By day 3 post immunization, we sort-purified NP-binding B cells that were developing into GCs and conducted RNA-seq analyses of their transcriptome. NP+IgDlowB220+ pre-GC B cells from recipients of the same group were pooled to sort-purify 4 200-cell repeats. Using a gene expression signature induced by CD40 signaling in B cells for enrichment analysis, we found such CD40-induced gene set expression was significantly deprived in those NP-binding B cells helped by CD4-Cre´Bcl6fl/+ T cells. These data suggest BCL6 insufficiency in T cells leads to impaired CD40L signaling to B cells.

2021-07-30 | GSE180833 | GEO

OT-I T cell activation in Lrrc8af/f and Lrrc8af/f Cd4-Cre;OT-I mice

Project description:Splenocytes were separated from Lrrc8af/f and Lrrc8af/f Cd4-Cre;OT-I mice. The splenocytes were stimulated with indicated peptides (unstime/ SIINFEKL-10pM(NL)/ SIINFEKL-1000pM(NH)/ SIIGFEKL-1000nM(G4)) for 6 hours. The OT-I CD8+ T cells were labeled with Va2-PE/CD8-A700 and sorted for the sequencing.

2023-09-26 | GSE243985 | GEO

OT-I T cell activation in Lrrc8af/f and Lrrc8af/f Cd4-Cre OT-I mice

Project description:OT-I T cell activation in Lrrc8af/f and Lrrc8af/f Cd4-Cre OT-I mice

| PRJNA1020844 | ENA

Gene expression profiling in mature OT-II TCR transgenic CD4 SP thymocytes, either Jmjd3- and Utx-deficient or -sufficient.

Project description:The biological functions of histone demethylases Jmjd3 and Utx remain poorly understood. We assessed such functions in developing T cells, using conditional (CD4-Cre-mediated) gene disruption, by inactivating Kdm6a and Kdm6b, respectively encoding Utx and Jmjd3, in immature CD4+CD8+ thymocytes. We compared microarray gene expression in mature (Va2hi CD24lo) mutant and wild-type CD4+CD8- thymocytes carrying the OT-II TCR transgene. We show that Jmjd3 and Utx redundantly promote H3K27Me3 removal at, and expression of, a specific subset of genes involved in terminal thymocyte differentiation, especially S1pr1, encoding a sphingosine-phosphate receptor required for thymocyte egress. Mature (Va2hi CD24lo) CD4 thymocytes were sorted from freshly prepared single-cell suspensions OT-II TCR transgenic thymocytes deficient for Utx and Jmjd3 (dKO, CD4-Cre conditional deletion of floxed Kdm6a and Kdm6b alleles), and from Cre-negative controls (wild-type). Total RNA was extracted from sorted thymocytes using the RNeasy Plus Mini Kit (Qiagen) and processed for microarray analyses (Affymetrix Mouse Exon 1.0 ST array) at the NCI microarray facility, following the manufacturer’s recommendation. Data is generated from 3 replicates from each experiment.

2015-09-17 | E-GEOD-70363 | biostudies-arrayexpress

RNA-sequencing of BCL6-sufficient and -insufficient OT-II TFH cells

Project description:We analyzed the transcriptome differences of BCL6-sufficient (CD4-Cre) and -insufficient (CD4-CrexBcl6fl/+) OT-II TFH cells. CD4-CrexBcl6fl/+ or control CD4-Cre OT-II T cells were transferred into CD45.1 Sap-/- mice. At day 3 post NP-OVA immunization, CXCR5hiPD-1hi TFH cells were sort-purified from the draining lymph node and prepared for RNA-seq analysis. Two technical repeats of ~200 cells per sample from each of 3 mice were included. BCL6-insufficient TFH cells differentially expressed many genes; among those downregulated were Stim1 and Plcg1, which code for STIM1 and PLCg1, respectively, that both impinge on calcium signaling downstream of TCR activation. Moreover, KEGG pathway analyses revealed that the calcium signaling-related pathway was generally upregulated in wildtype as compared to BCL6-insufficient TFH cells. These data support the notion that BCL6 control follicular T-B interactions by regulating multiple target genes involved in antigen-triggered calcium signaling in T cells.

2021-07-30 | GSE180924 | GEO

Gene expression profiling in mature OT-II TCR transgenic CD4 SP thymocytes, either Jmjd3- and Utx-deficient or -sufficient.

2015-09-17 | GSE70363 | GEO

Regulation ot TAM gene expression by ABCA1 and ABCG1 (4 Cre- and 4 Cre+)

Project description:Regulation ot TAM gene expression by ABCA1 and ABCG1 (4 Cre- and 4 Cre+)

| PRJNA520922 | ENA

pre-GC and GC B cell scRNAseq

Project description:pre-GC and GC B cell scRNAseq

| PRJNA973113 | ENA

RNA seq of vhlfl/fl cd4 cre, hif1afl/fl vhlfl/fl cd4 cre and WT CD4 T cells before and after anti-CD3/CD28 stimulation

Project description:Purpose: We compared the transcriptomes of murine CD4 T cells lacking either the vhl gene ( vhlfl/fl cd4 cre (vhl cKO) ) or both vhl and hif1a (hif1afl/fl vhlfl/fl cd4 cre (dcKO)) with WT controls before and 24 h after T cell receptor stimulation using anti-CD3/CD28. Results: Using an optimized data analysis workflow, about 45-60 million sequence reads per sample to the mouse genome (build mm10) and identified ca 12500 transcripts in the CD4 T cells of WT and mutant mice after performing HISAT2 alignements to the mm10 reference. Conclusion: the segregation of the transcriptome of unstimulated WT CD4 T cells as compared to the other groups. Within the TCR-stimulated groups the gene expression of vhl cKO CD4 T cells differed to that of WT and vhl hif1a dcKO CD4 T cells which showed in comparison important similarity between them

2022-06-01 | GSE190791 | GEO

Memory OT-I cells

Project description:Memory OT-I cells

| PRJNA639155 | ENA