Expression analysis of TCRgd+LAP+ versus TCRgd+LAP- cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE73077 | GEO | 2015/09/17
SECONDARY ACCESSION(S): PRJNA296054
REPOSITORIES: GEO
Similar Datasets
Project description:We used RNA-Seq to identify differential gene expression in LAP+ vs. LAP- Gamma-delta T-cells. We report a signature of 407 genes that were enriched in TCRgd+LAP+ vs. TCRgd+LAP- cells with p<0.05. Among the up-regulated genes, we found increased expression of genes related to antigen presentation, including MHC class II molecules (H2-Aa, H2-Ab1, H2-Eb1 and H2-Eb2), CD40 and CD86 RNA-Seq of TCRgd+LAP+ versus TCRgd+LAP- cells harvested from mouse spleen and Peyer's patches; began with 20 mice for two independent experiments (10 mice each); samples were pooled and for each experiment resulted in one LAP- and one LAP+ sample for RNA-SEQ, or four samples in total; The two LAP+ were combined, resulting in three samples in total for RNA-Seq.
2015-09-17 | E-GEOD-73077 | biostudies-arrayexpress
Project description:Expression analysis of TCRgd+LAP+ versus TCRgd+LAP- cells
| PRJNA296054 | ENA
Project description:BACKGROUND & AIMS: C/EBPbeta is involved in numerous process as carcinogenesis but its role is still not clear due to the existence of an active form (LAP) and an inhibitory form (LIP) of this transcription factor. The main goals of the present research were (i) the identification of genes inversely regulated by LAP and LIP i-e the genuine C/EBPbeta molecular signature in the Hep3B human hepatoma cell line (ii) a better understanding of LAP and LIP respective role in hepatic cells survival and proliferation (iii) the search of the C/EBPbeta signature among hepatocellular carcinomas. METHODS: Using Tet-off expression system we engineered Hep3BLAP and Hep3BLIP cells, in which LAP and LIP were over-expressed respectively. Then, using both expression profiling (DNA arrays) and ChIP-on-chip analysis, we identified genes inversely and/or directly regulated by each of the C/EBPbeta isoforms. The expression levels of these genes regulated by LAP/LIP were compared in controls and HCCs patients. RESULTS: We identified 676 genes inversely regulated by LAP and LIP and among these, 45 are direct targets. Using functional studies, we displayed the opposite role of LAP and LIP in staurosporine-induced cell death and the implication of LAP in the repression of Hep3B cells proliferation. Finally we identified a subgroup of HCCs with a deregulation of 165 genes belonging to C/EBPbeta signature and coding for proteins involved in chemoresistance and metastasis formation. CONCLUSIONS: Our study increases knowledge on LAP and LIP functions and provides first evidence that their molecular signature in the HCCs could predict tumor evolution.
2009-02-27 | GSE15010 | GEO
Project description:We looked for parent of origin effects on genome-wide gene expression in a reciprocal cross between C57BL/6J x B6(C)-H2bm12/KhEgJ mice (the latter strain is a knockout of H2-ab1 on a C57BL/6J background). The aim is to find genes whose expression is altered in trans depending on whether the mother or father carried a knockout allele for H2-ab1. In this experiment differential expression of a gene is inferred from a difference in its overall expression levels. We sequenced RNA from 30 F1 mice from the H2-ab1 heterozygous cross. Both heterozygous and wild type F1 animals were sequenced in order to find both parental and parent of origin effects. We measured expression in the lungs (average 6.2 million reads per sample) and hippocampus (6.6 million reads).
2013-11-01 | E-MTAB-1998 | biostudies-arrayexpress
Project description:BACKGROUND & AIMS: C/EBPbeta is involved in numerous process as carcinogenesis but its role is still not clear due to the existence of an active form (LAP) and an inhibitory form (LIP) of this transcription factor. The main goals of the present research were (i) the identification of genes inversely regulated by LAP and LIP i-e the genuine C/EBPbeta molecular signature in the Hep3B human hepatoma cell line (ii) a better understanding of LAP and LIP respective role in hepatic cells survival and proliferation (iii) the search of the C/EBPbeta signature among hepatocellular carcinomas. METHODS: Using Tet-off expression system we engineered Hep3BLAP and Hep3BLIP cells, in which LAP and LIP were over-expressed respectively. Then, using both expression profiling (DNA arrays) and ChIP-on-chip analysis, we identified genes inversely and/or directly regulated by each of the C/EBPbeta isoforms. The expression levels of these genes regulated by LAP/LIP were compared in controls and HCCs patients. RESULTS: We identified 676 genes inversely regulated by LAP and LIP and among these, 45 are direct targets. Using functional studies, we displayed the opposite role of LAP and LIP in staurosporine-induced cell death and the implication of LAP in the repression of Hep3B cells proliferation. Finally we identified a subgroup of HCCs with a deregulation of 165 genes belonging to C/EBPbeta signature and coding for proteins involved in chemoresistance and metastasis formation. CONCLUSIONS: Our study increases knowledge on LAP and LIP functions and provides first evidence that their molecular signature in the HCCs could predict tumor evolution. Total genomic DNA were extracted from 3 Hep3BLAP expressing LAP and were labelled Cy3 fluorochrome. Genomic DNA were extracted from 3 Hep3BLAP expressing LAP, were immunoprecipited with anti-CEBPbeta antibody and were labelled with Cy5 fluorochrome. Each sample was hybridized on an Agilent two-color microarray G4489A (Human Promoter ChIP-on-Chip Set 244K).
2010-05-22 | E-GEOD-15010 | biostudies-arrayexpress
Project description:PECs from wild-type, NF-IL6KO and KI(LAP) mice were stimulated with or without LPS+IFN-gamma for 12h. We used microarrays to check the difference of gene induction among wild type, KO and KI mice. Keywords: Wild, KO and KI(LAP)
2007-12-05 | GSE7649 | GEO
Project description:Aging is associated with increased monocyte production and altered monocyte function. Classical monocytes are heterogenous and a shift in their subset composition may underlie some of their apparent functional changes during aging. We have previously shown that mouse granulocyte-monocyte progenitors (GMPs) produce “neutrophil-like” monocytes (NeuMo), whereas monocyte-dendritic cell progenitors (MDPs) produce monocyte-derived dendritic cell (moDC)-producing monocytes (DCMo). Here, we demonstrate that classical monocytes from the bone marrow of old male and female mice have higher expression of DCMo signature genes (H2-Aa, H2-Ab1, H2-Eb1, Cd74), and that more classical monocytes express MHCII and CD74 protein. Moreover, we show that bone marrow MDPs and classical monocytes from old mice yield more moDC. We also demonstrate higher expression of Aw112010 in old monocytes and that Aw112010 lncRNA activity regulates MHCII induction in macrophages, which suggests that elevated Aw112010 levels may underlie increased MHCII expression during monocyte aging. Finally, we show that classical monocyte expression of MHCII is also elevated during healthy aging in humans. Thus, aging-associated changes in monocyte production may underlie altered monocyte function and have implications for aging-associated disorders.
2022-08-30 | GSE207063 | GEO
Project description:To compare tumor associated macrophage (TAM) from naïve and sepsis surviving mice we have employed Agilent microarrays slides with almost 60,000 genes (39,430 mRNA and 16,251 long non coding RNAs). Other experiments we conducted demonstrated TAM accumulation was increased in post-sepsis subjects. For this reason, we asked if TAM from post-sepsis mice could also exhibit a different gene expression profile. Sepsis was induced by cecal and ligation puncture. Naïve mice were used as control group. All animals were treated with ertapenem (20 mg/kg, i.p., 6 hours after surgery, and then each 12 hours for 3 days). B16-F10 melanoma (30,000 cells) were injected subcutaneously at day 14 after sepsis induction. Fourteen days after tumor inoculation, animals were killed and tumors were harvested and digested (collagenase and DNAse). TAM was isolated by a Percoll gradient (70/30) followed by a 1-hour adhesion protocol, reaching a purity of ~75%. For comparative reasons, we assessed TAM from post-sepsis (n = 4), TAM from naïve mice (n = 4), bone marrow derived macrophage from naïve (n = 4) and from post-sepsis (n = 4), M1-polarized macrophage (n = 4) and M2-polarized macrophage (n = 4). We found only minor gene expression differences between TAM from naïve and from post-sepsis mice (61 genes were up-regulated and 98 genes were down-regulated, fold-change > 0.58 or < -0.58, and p < 0.01). We found genes related to leukocyte activation were down-regulated in TAM from post-sepsis mice (e.g. Ccr7, Cd86, H2-Ab1), as well as genes related to antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (H2-DMb1, Cd74, H2-Eb1, H2-Ob). A gene related to M2 polarization was up-regulated (Marco). Also, we found a down-regulation of Nfkbid in post-sepsis-derived TAM. This led us to hypothesize TAM from post-sepsis mice exhibit a more M2-like phenotype, which may in part contribute to post-sepsis tumor expansion. Three independent experiments were conducted for TAM obtaining, each experiment using n = 4 for naïve and n = 4 for post-sepsis. We selected the 4 best within a group of 12 samples, following A260/280 and A260/230 ratios. For bone marrow derived macrophage from naïve and from post-sepsis, and for M1 and M2-polarized macrophage, we conducted two independent experiments using n = 3 per group. The best 4 samples in each group was selected to microarray processing and analysis.
2014-12-25 | E-GEOD-64498 | biostudies-arrayexpress
Project description:To compare tumor associated macrophage (TAM) from naïve and sepsis surviving mice we have employed Agilent microarrays slides with almost 60,000 genes (39,430 mRNA and 16,251 long non coding RNAs). Other experiments we conducted demonstrated TAM accumulation was increased in post-sepsis subjects. For this reason, we asked if TAM from post-sepsis mice could also exhibit a different gene expression profile. Sepsis was induced by cecal and ligation puncture. Naïve mice were used as control group. All animals were treated with ertapenem (20 mg/kg, i.p., 6 hours after surgery, and then each 12 hours for 3 days). B16-F10 melanoma (30,000 cells) were injected subcutaneously at day 14 after sepsis induction. Fourteen days after tumor inoculation, animals were killed and tumors were harvested and digested (collagenase and DNAse). TAM was isolated by a Percoll gradient (70/30) followed by a 1-hour adhesion protocol, reaching a purity of ~75%. For comparative reasons, we assessed TAM from post-sepsis (n = 4), TAM from naïve mice (n = 4), bone marrow derived macrophage from naïve (n = 4) and from post-sepsis (n = 4), M1-polarized macrophage (n = 4) and M2-polarized macrophage (n = 4). We found only minor gene expression differences between TAM from naïve and from post-sepsis mice (61 genes were up-regulated and 98 genes were down-regulated, fold-change > 0.58 or < -0.58, and p < 0.01). We found genes related to leukocyte activation were down-regulated in TAM from post-sepsis mice (e.g. Ccr7, Cd86, H2-Ab1), as well as genes related to antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (H2-DMb1, Cd74, H2-Eb1, H2-Ob). A gene related to M2 polarization was up-regulated (Marco). Also, we found a down-regulation of Nfkbid in post-sepsis-derived TAM. This led us to hypothesize TAM from post-sepsis mice exhibit a more M2-like phenotype, which may in part contribute to post-sepsis tumor expansion.
2014-12-25 | GSE64498 | GEO
Project description:[Purpose] To define the traditional profile of EcTMs, RNA seq analysis were parformed on EcTMs and non EcTMs at postnatal day28. [Method] The workflow consists of first-strand synthesis, template switching, adaptor ligation, cleavage of ribosomal cDNA and PCR amplification. Different adaptors were used for multiplexing samples in one lane. Sequencing was performed on an Illumina Nextseq500 a single read 75 run. Data quality check was conducted on Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program. Reads were aligned to the UCSC mm10 reference genome map using TopHat. DEseq2 was used to identify differentially expressed genes of EcTMs compared to non-EcTMs. 36 upregulated genes in EcTMs compared to non-EcTMs with a padj < 0.05 were subsequently clustered and visualized using R. Gene ontology functional analyses were performed using the database for annotation, visualization, and integrated discovery (DAVID) online tool.[Result] 40 genes were differentially expressed between the two groups: 36 were higher and 4 genes were lower in EcTMs compared to non-EcTMs. Gene Ontology analysis revealed that EcTMs were enriched for genes related to antigen presentation, lysosomes, and phagosomes (H2-Ab1, H2-Aa, H2-Eb1, CD74, Laptm5). [Conclusion] EcTMs would have higher potential for presenting antigen and phagositosis compared to non EcTMs.
2019-02-27 | GSE100495 | GEO