Trerf1 knockout compared to wild type lineage-negative CD127+ bone marrow cells
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PROVIDER: PRJNA846277 | ENA |
REPOSITORIES: ENA
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Project description:Mice that lack the transcriptional regulator Trerf1 lack ILC1 in the liver and immature ILC1 in the bone marrow. To determine which pathways are downstream of Trerf1, we sorted lineage-negative CD127+ bone marrow cells (which contain ILC progenitors) from 4 littermate pairs (wild type versus Trerf1 knockout) and examined them by RNAseq.
2022-06-09 | GSE205528 | GEO
Project description:Group 2 Innate Lymphoid Cells (ILC2s) are key players in type 2 immunity and contribute to maintaining homeostasis and responding to inflammation. ILC2s are implicated in the development of type 2 inflammation-mediated chronic disorders like asthma. While memory ILC2s have been identified in mouse, it is unknown whether human ILC2s can acquire immunological memory. Here, we demonstrate the persistence of CD45RO, a marker previously linked to inflammatory ILC2s, in resting ILC2s that have undergone prior activation. A high proportion of these cells concurrently reduce the expression of the canonical ILC marker CD127 in a tissue specific manner. Through isolation and in vitro stimulation of CD127- CD45RO+ ILC2s, we observed an augmented ability to proliferate and produce cytokines. CD127- CD45RO+ ILC2s are found in both healthy and inflamed tissues and display a gene signature of cell activation. Our findings suggest that human ILC2s can acquire innate immune memory and warrants a revision of the current strategies to identify human ILC2s.
2024-05-20 | GSE267098 | GEO
Project description:Background: Alternaria exposure is associated with severe asthma in humans. Alternaria exposure in mice potently activates group 2 innate lymphoid cells (ILC2s) via the IL-33/ST2 axis and causes ILC2s to robustly secrete type 2 cytokines. Objective: Our aim was to determine whether conventionally used ILC2 markers, ST2 (IL-33R) and CD127 (IL-7Ra), were sufficient to identify all Th2-cytokine producing ILCs after Alternaria exposure. Methods: Mice received intranasal Alternaria for three days prior to analysis. Lung ILCs were identified by flow cytometry as CD45+Lineage−Thy1.2+ lymphocyte-sized cells, divided into four subsets based on ST2 and CD127 expression, and stained for intracellular cytokines and transcription factors. Sort-purified ILC subpopulations were also analyzed by RNA sequencing and qPCR. Results: Alternaria exposure led to accumulation of all ILC populations regardless of ST2 or CD127 expression. Nearly half of the GATA-3+, IL-5+, and IL-13+ ILCs were “unconventional” as they were either single or double negative for ST2/CD127. Further, these populations upregulated CD25, KLRG1, and ICOS after Alternaria challenge. Some activated unconventional IL-5+ ILC2s also produced IFNγ and IL-17A. In addition to shared ILC2 transcripts (Gata3, Il5, Il13) in all populations, RNA-seq further identified novel transcripts enriched in each subset. Finally, transcripts from all populations that correlated best with IL-5 and IL-13 production included Tnfrsf18, Ffar2, and Pde4b. Conclusions: Unconventional ST2- and CD127-negative mouse lung ILC2 populations are induced by Alternaria. Thus, commonly used lung ILC2 identification methods based on ST2 and CD127 do not accurately account for the total ILC2 burden and may exclude nearly half of these cells.
2019-08-22 | GSE136156 | GEO
Project description:Hdac3 is highly expressed in pDCs, and its deficiency led to substantially impaired development of pDCs, but not cDCs in bone marrow (BM) and spleen. Meanwhile,further investigation demonstrated that HDAC3 was required for the differentiation of pDC from progenitors at different differentiation stages in vitro. Cut & Tag analysis of H3K27ac level in HDAC3 deficient bone marrow pDCs compared with control pDCs, showed that H3K27ac level significantly increased on cDC related genes with PU.1 binding sites in HDAC3 knockout pDCs.
2022-05-27 | GSE197212 | GEO
Project description:To understand differences between resting and activated memory CD8+ T cells, we compared the global gene expression of ex vivo isolated naive and spleen and BM memory cells to in vitro activated spleen and BM memory cells. Single cell suspension from the spleen and bones of aged C57BL/6 mice were prepared. Naive (CD44-CD127+) and memory (CD44+CD127+) CD8+CD3+ T cells were then cytometrically sorted. Sorted cells were either immediately processed for RNA preparation or were activated with anti-CD3 and anti-CD28 for 42-44 hours. Total RNA was extracted using the NucleoSpin RNA (Macherey-Nagel). The integrity and amount of isolated RNA was assessed for each sample using an Agilent 2100 Bioanalyzer (Agilent, Waldbronn, Germany) and a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). Double-stranded complementary RNA was synthesized from 1 M-BM-5g total RNA using Message AmpII Biotin (Ambion, USA). Fifteen micrograms of fragmented cRNA of each sample were hybridized to MG_U430_2 GeneChips (Affymetrix) in triplicates. Hybridization was performed in a Hybridization Oven 640, and chips were washed and stained in the Fluidics Station 400 (both Affymetrix). Finally, the arrays were scanned with a GeneChip Scanner 3000 using the GCOS software, version 1.4, both Affymetrix. All relevant GCOS data of quality checked microarrays were analyzed with High Performance Chip Data Analysis (HPCDA, unpublished), using the BioRetis database (www.bioretis-analysis.de), as described and validated previously.
2015-02-05 | E-GEOD-62691 | biostudies-arrayexpress
Project description:Single cell transcriptomic analysis of human CD25+ CD127- CD4+ Treg cells and CD25- CD127+ CD4+ Tconv cells isolated from peripheral blood from two different donors
2018-03-15 | GSE111901 | GEO
Project description:Clostridioides difficile CD127 Genome sequencing and assembly
| PRJNA85741 | ENA
Project description:We derived B-lineage cells by in vitro culture of neonatal cord blood CD34+ cells on MS-5 stromal cells with recombinant IL-7. These cultures yielded CD19+CD127+ and CD19+CD127- cell populations. We performed gene expression profiling on these populations and compared these with each other and with published expression profiles of freshly isolated BM precursor B-cell subsets (E-MEXP-384). These analyses yielded new insights into their different functionality and developmental stage.<br><br>A file containing statistical analysis of the normalized data is included in the file named E-MEXP-2878.additional.zip on the FTP site for this experiment.
2011-01-01 | E-MEXP-2878 | biostudies-arrayexpress
Project description:Osteoclast differentiation and activation requires the presence of osteoblast-derived factors such as Macrophage colony stimulating factor (M-CSF) and receptor activator of nuclear factor-kappaB ligand (RANKL). RANKL is influenced by osteotropic hormones such as calcitriol 1,25(OH)2D3 (vitamin D).The aim of this study is to evaluate the combined effect of vitamin D and M-CSF on murine bone marrow and on murine spleen cell, to define when the inhibitory effect of vitamin D plus M-CSF is maximum and what are the mechanisms involved in this inhibition. When murine bone marrow cells were cultured with 10-8 M vitamin D and 60 ng/ml M-CSF, there was a significant decrease in osteoclasts formation (3.13±3.44),compared to bone marrow cells cultured with vitamin D alone (80.86 ±45.02; p<0.05). Even when the amount of M-CSF added to the bone marrow cell culture was 1 ng/ml there was a 40% decrease in osteoclasts formation. Since bone marrow contains also stromal cells, we eliminate their influence by culturing murine spleen cells with 10-8 M vitamin D, 60 ng/ml M-CSF and RANKL 20 ng/ml. There was a significant decrease in osteoclasts formation (41±14.14) compared to spleen cells cultured with M-CSF and RANKL (215.67±46.44); p<0.05). These data lead to hypothesize that vitamin D and M-CSF together exert an inhibitory effect on osteoclast differentiation and development. To define the cellular mechanism involved in this inhibition we analyzed gene array data of bone marrow cells cultured with vitamin D and compare them with the cells cultured with vitamin D and M-CSF. Activation Toll like receptors after addition of vitamin D plus M-CSF to bone marrow cells appears to be involved in the inhibition of osteoclast differentiation. Keywords: parallel sample
2004-08-31 | GSE1587 | GEO
Project description:Analysis of global RNA expression of Cebpa knockdown lineage-negative marrow cells reveals known and potentially novel C/EBPa targets. Total RNA from lineage-negative marrow progenitors transduced with vector or Cebpa shRNA and cultured under myeloid differentiation condition for 2 days were compared.
2014-03-11 | E-GEOD-55760 | biostudies-arrayexpress