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RNA-seq analysis of bead-purified B cells of wild-type BALB/c mice stimulated in vitro with TLR9 agonists (CpG ODN 1826, Hokkaido System Science) or left unstimulated.

ABSTRACT: RNA-seq analysis of bead-purified B cells of wild-type BALB/c mice stimulated in vitro with TLR9 agonists (CpG ODN 1826, Hokkaido System Science) or left unstimulated.

PROVIDER: PRJNA1122066 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR29341106.fastq.gz	Fastqsanger.gz
	SRR29341106_1.fastq.gz	Fastqsanger.gz
	SRR29341106_2.fastq.gz	Fastqsanger.gz
	SRR29341107.fastq.gz	Fastqsanger.gz
	SRR29341107_1.fastq.gz	Fastqsanger.gz

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RNA-seq analysis of bead-purified B cells of wild-type BALB/c mice stimulated in vitro with TLR9 agonists (CpG ODN 1826, Hokkaido System Science) or left unstimulated.

Project description:The goal of this study was to develop a B-cell specific gene signature to catalog induced genes after short term in vitro TLR9 stimulation of wild-type BALB/c B cells. B cells were bead purified from splenocytes (two spleens combined for one replicate) of 7-11-week-old wild-type BALB/c mice. The bead purified B cells (10 million (M) per replicate) were stimulated for 4 hours at 10M/ml with TLR9 agonist CpG (CpG ODN 1826, Hokkaido System Science) at 10µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN). Samples were sequenced on an NextSeq500 (Illumina, Inc) with 2 x 75 bp paired-end reads (20 million reads per sample). B-cell specific gene signature of induced genes after short term in vitro TLR9 stimulation was cataloged.

2024-12-31 | GSE269458 | GEO

RNA-seq analysis of bead-purified B cells of (i) 5-7-week-old Tlr779 or Tlr7WT (all Tlr9-/-) MRL/lpr mice

Project description:RNA-seq analysis of bead-purified B cells of (i) 5-7-week-old Tlr779 or Tlr7WT (all Tlr9-/-) MRL/lpr mice,stimulated or not with TLR7 agonists (CL097, invivogen) and of (ii) 5-7-week-old Tlr997 or Tlr9+/- (all Tlr7-/-) MRL/lpr mice, stimulated or not with CpG (ODN 1826, Hokkaido System Science) . The goal of this study was to evaluate if CL097 or CpG induced qualitatively different responses in Tlr7WT or Tlr779 (all Tlr9-/-) B cells and in Tlr9+/- or Tlr997 (all Tlr7-/-) B cells, respectively.

2024-12-31 | GSE269457 | GEO

RNA-seq analysis of bead-purified B cells of 5-week-old TLR9-/- MRL/lpr mice stimulated in vitro with TLR7 agonists (CL097, invivogen) or left unstimulated.

Project description:Purpose: The goal of this study was to develop a B-cell specific gene signature to catalog induced genes after short term in vitro TLR7 stimulation of TLR9-/- MRL/lpr B cells. Methods : Bead purified B cells (5M) from three 5-week-old TLR9-/- MRL/lpr mice were stimulated for 4 hours at 10M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Mini Kit (QIAGEN). Samples were sequenced on an NextSeq500 (Illumina, Inc) with 2 x 75 bp paired-end reads (20 million reads per sample). Results: a B-cell specific gene signature of induced genes after short term in vitro TLR7 stimulation was cataloged.

2022-08-03 | GSE202108 | GEO

Transcription profiling by sequencing of murine MyD88 -/- and MyD88 +/+ mTECs stimulated with a TLR9 ligand

Project description:We compared in vitro mTECs-high stimulated with TLR9 ligand CpG ODN (1826) or non stimulated from MyD88 -/- and MyD88 +/+ mice: Thymi were enzymaticaly digested, cells were MACS enriched for CD45- fraction, and FACS sorted using BD Influx sorter. mTECs-high were gated as EpCAM+CD11c-Ly51-MHCII+CD80+. Cell from MyD88 -/- and MyD88 +/+ mice were incubated in RPMI with or without CpG ODN (1826) for 24 hours. Total RNA was isolated using RNeasy Plus Micro Kit (Qiagen). 4 samples per condition were used.

2020-03-20 | E-MTAB-8025 | biostudies-arrayexpress

IRF-5 and IRF-8 govern the response of Human Plasmacytoid Dendritic Cells following TLR9 ligation

Project description:Synthetic oligonucleotides (ODNs) containing CpG motifs stimulate human plasmacytoid dendritic cells (pDCs) to produce type-1 interferons (IFN) and pro-inflammatory cytokines. Previous studies demonstrated that interferon regulatory factors (IRFs) played a central role in mediating CpG-induced pDC activation. This work explores the inverse effects of IRF-5 and IRF-8 on CpG dependent gene expression. Results from RNA interference and microarray studies indicate that IRF-5 up-regulates TLR9-driven gene expression whereas IRF-8 down-regulates the same genes. Several findings support the conclusion that IRF-8 inhibits TLR9 dependent gene expression by directly blocking the activity of IRF-5. First, the inhibitory activity of IRF-8 is only observed when IRF-5 is present. Second, proximity ligation analysis shows that IRF-8 and IRF-5 co-localize within the cytoplasm of resting human pDC and co-translocate to the nucleus after CpG stimulation. Taken together, these findings suggest that two transcription factors with opposing functions control TLR9 signaling in human pDCs. CAL-1 cells were transfected with siRNA targeting IRF-5 (IRF-5si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with siRNA targeting IRF-8 (IRF-8si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with control siRNA (Contsi) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats).

2016-06-01 | E-GEOD-70429 | biostudies-arrayexpress

Short and long-term changes in gene expression mediated by the activation of TLR9

Project description:CpG DNA binds to Toll-like receptor 9 to stimulate a strong innate immune response. Despite extensive studies of TLR9 mediated signal transduction, the scope of CpG-induced changes in gene expression is incompletely understood. In particular, the prolonged effects of CpG ODN (oligodeoxynucleotide) on gene activation have not been investigated despite evidence that a single dose of CpG ODN alters immune reactivity for several weeks. This study used gene expression analysis to monitor changes in mRNA levels for 14 days, and identified the genes, pathways, functional groups and regulatory networks triggered in vivo following CpG ODN administration. Two discrete peaks of gene activation (at 3 hr and 5 days) were observed after CpG administration. Both the regulation and function of genes activated during the second peak differed from those triggered shortly after CpG administration. Initial gene up-regulation corresponded to a period when TLR9 ligation stimulated genes functionally associated with the generation of innate and adaptive immune responses (e.g. the NF-kB and B-cell receptor pathways). The second peak reflected processes associated with cell division (e.g., cell cycle and DNA replication & repair). Whereas TNF and IFNG played central roles regulating the first peak of activation, E2F1, E2F2, BRCA1, and HRAS had major impact on the networks controlling the second peak. The complex bimodal pattern of gene expression elicited by CpG ODN administration provides novel insights into the long term effects of CpG DNA on genes associated with immunity and cell proliferation.

2010-01-08 | GSE16465 | GEO

Short and long-term changes in gene expression mediated by the activation of TLR9

2010-05-16 | E-GEOD-16465 | biostudies-arrayexpress

IGROV1 miRNA expression analysis after in vivo locoregional treatment with CpG-ODN

Project description:We reported that peri-tumoral CpG-ODN treatment, probably activating TLR9-expressing cells present in the tumor microenvironment, sensitized cancer cells to DNA-damaging chemotherapy (Cancer Res 2011 Oct 15;71(20):6382-90). Here, we investigated whether this treatment induces a modulation of miRNAs and their involvement in chemotherapy sensitivity. Twenty miRNAs were found differentially expressed in tumors from CpG-ODN-treated mice versus controls. Evaluation of the role of miR-424, miR-340 and miR-302b on cisplatin sensitivity revealed that ectopic expression of miR-302b (up-modulated in our array) in IGROV1 cells significantly improved cisplatin activity. The identification of miRNAs able to modify sensitivity to chemotherapy treatment will provide an experimental base for its future possible use as a target or tool of specific therapies.

2013-03-31 | GSE41783 | GEO

Project description:Toll-like receptors (TLRs) are mediators in the innate immune response by recognizing nucleic acids derived from microbial components as for TLR9 binding ability for CpG rich bacterial DNA. We studied the differential expression by microarrays of all known T-UCRs and near genes in a series of 6 primary B-CLL cases cells comparing cells treated in vitro with CpG ODN versus mock controls.

2018-12-31 | GSE57160 | GEO

RNA-seq analysis of follicular (FO) and marginal zone (MZ) B cells, isolated from TLR9WT or TLR9-/- BALB/c mice, stimulated with TLR7 agonists (CL097, Invivogen) or left unstimulated .

Project description:Purpose: The goal of this study was to assess if increased TLR7 signaling could be seen in TLR9-/- compared to TLR9WT FO and MZ B cells. Methods : FO and MZ B cells from TLR9WT or TLR9-/- BALB/c mice were sorted using FACSaria. A minimum of 100,000 cells per B cell subsets were sorted. Sorted B cell subsets were stimulated for 4 hours at 0.25M/ml with TLR7 agonist CL097 (Invivogen) at 5µg/ml or left unstimulated. RNA was isolated using the RNeasy Plus Micro Kit (QIAGEN). Samples were sequenced on an Illumina Next-seq 2000 using a P3 200 cycle flowcell (Illumina, Inc) with 2 x 101 bp paired-end reads (20 million reads per sample). Results: There were no significant DEG (FDR > 0.05) following TLR7 stimulation between TLR9WT and TLR9-/- FO or MZ B cells.

2022-08-03 | GSE202105 | GEO

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