Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13488429_1.fastq.gz | Fastqsanger.gz | |||
| SRR13488429_2.fastq.gz | Fastqsanger.gz | |||
| SRR13488430_1.fastq.gz | Fastqsanger.gz | |||
| SRR13488430_2.fastq.gz | Fastqsanger.gz | |||
| SRR13488431_1.fastq.gz | Fastqsanger.gz |
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Project description:Both mHSCs and nHSCs had activated differentiation genes upon LM challenge; however, mHSCs more robustly increased cell cycle and T lymphocyte-differentiation genes but reduced myeloid-, erythrocyte- and B cell-differentiation genes compared to nHSCs upon LM challenge
2024-05-02 | GSE202099 | GEO
Project description:Both mHSCs and nHSCs had activated differentiation genes upon LM challenge; however, mHSCs more robustly increased cell cycle and T lymphocyte-differentiation genes but reduced myeloid-, erythrocyte- and B cell-differentiation genes compared to nHSCs upon LM challenge
2024-05-02 | GSE202142 | GEO
Project description:Both mHSCs and nHSCs had activated differentiation genes upon LM challenge; however, mHSCs more robustly increased cell cycle and T lymphocyte-differentiation genes but reduced myeloid-, erythrocyte- and B cell-differentiation genes compared to nHSCs upon LM challenge
2023-05-16 | GSE203129 | GEO
Project description:Uterine leiomyoma (LM) is the most common tumor in women. Estrogen and progesterone, via their receptors ERα and PR, play essential roles in LM growth. Mediator complex subunit 12 (MED12) mutations occur in 70% of all LM and are thought to drive tumor growth in a steroid hormone-dependent manner; however, the mechanisms remain unclear. Here, we performed ChIP-seq (ERα, PR, and MED12) and RNA-seq on LM expressing mutant MED12 (mut-MED12) or wild-type MED12 and matched myometrium. Mut-MED12 altered PR and chromatin interaction landscapes, with significant PR-binding site loss in proximal promoter regions in mut-MED12 LM. Integration of cistrome and transcriptome data identified tryptophan 2,3-dioxygenase (TDO2) as a PR and MED12 target gene, which was aberrantly upregulated in mut-MED12 LM. Kynurenine, the catabolic product of TDO2, was significantly elevated in mut-MED12 LM. Tryptophan or kynurenine treatment of primary LM cells activated the aryl hydrocarbon receptor (AHR) pathway, increased cell proliferation, and inhibited apoptosis; blocking the TDO2-kynurenine-AHR pathway by siRNA knockdown or pharmacologic inhibition abolished these effects. Mut-MED12 LM cells showed higher sensitivity to these treatments. These findings suggest that activation of the TDO2-kynurenine-AHR pathway in mut-MED12 LM induces tumor growth, and may inform the development of targeted treatments and precision medicine in LM.
2023-05-01 | GSE204968 | GEO
Project description:Type 1 CD8α+ conventional dendritic cells (cDC1s) harbor and transport Listeria monocytogenes (LM) within the spleen and thereby promote infection; cDC1s are also required for CD8+ T cell priming. To test the role of the second lineage of splenic cDC in regulating infection or adaptive immunity to LM we used Dock8-deficient mice, which have impaired 33D1+ type 2 cDC (cDC2) function. We found reduced CD8+ T cell activation in Dock8-deficient mice, but this was not due to impaired cDC2 function but rather resistance to LM infection. Bacterial resistance was due to loss of marginal zone B (MZB) cells. We showed that IL-10 production by MZB cells did not alter antigen handling pathways in dendritic cells (DCs), including ones relevant for cross-priming or Listeria survival. Instead, IL-10 increased intracellular LM in macrophages in the marginal zone, which transfer bacteria to cDC1s. Bacteria-harboring cDC1s then traffic into the splenic white pulp where protection from sterilizing phagocytes promotes LM expansion. This work uncovers a unique crosstalk between the innate immune cells in the marginal zone, facilitated by IL-10, that promotes both infection but also CD8+ T cell activation.
2019-06-20 | GSE124771 | GEO
Project description:To identify lung metastasis associated microRNAs in triple negative breast cancer (TNBC), we have employed the commercially available Agilent Human miRNA V19.0 Microarray (Platform GPL19730) as a discovery platform. In comparison with LM-Normal, 11 microRNAs significantly altered in both LM-Met and LM-Tumor, and then three of them (hsa-miR-21-3p, hsa-miR-21-5p and hsa-miR-211-3p) were excluded, which were also up-regulated in RF-Tumor. Consequently, eight deregulated microRNAs were identified to be putatively involved in process of lung metastasis, especially miR-629-3p, which was most up-regulated in both LM-Met and LM-Tumor. To validate the microarray data, we utilized qRT-PCR to assess expression levels of the eight miRNAs in the same samples.
2016-04-08 | GSE80038 | GEO
Project description:Uterine leiomyosarcoma (LMS) is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM) is a benign tumor of myometrial origin and is the most common among women of childbearing age. Because the symptoms of women with LMS such as abnormal vaginal bleeding, palpable pelvic mass, and pelvic pain resemble with those of women with LM, it is difficult to preoperatively distinguish LMS and LM only by ultrasound and pelvic MRI. While histopathological diagnosis after hysterectomy is the current major means to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Furthermore, the low incidence of LMS has been preventing elucidating its causal mechanisms and developing effective diagnoses and treatments. Therefore, development of molecular diagnosis as an alternative or confirmatory means helps diagnosing LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM, and revealed that copy-number, gene expression, and DNA methylation profiles successfully distinguished between these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle –related genes, and hypomethylation spreading through large genomic regions as well as frequent hypermethylation at polycomb group target gene and cadherin gene loci. We also identified candidate expression and DNA methylation markers, which will help establishing diagnostic tests using conventional quantitative assays. While the identified omics-signatures and certain markers specific to LMS need to be further validated in larger numbers of LM and LMS samples, our results demonstrate the practical feasibility of establishing a postoperative diagnostic test to distinguish LMS from LM with high accuracy, and also suggest the future possibility of developing preoperative and non-invasive diagnostic methods.
2017-02-09 | GSE68295 | GEO
Project description:Uterine leiomyosarcoma (LMS) is the worst malignancy among the gynecologic cancers. Uterine leiomyoma (LM) is a benign tumor of myometrial origin and is the most common among women of childbearing age. Because the symptoms of women with LMS such as abnormal vaginal bleeding, palpable pelvic mass, and pelvic pain resemble with those of women with LM, it is difficult to preoperatively distinguish LMS and LM only by ultrasound and pelvic MRI. While histopathological diagnosis after hysterectomy is the current major means to distinguish them postoperatively, unusual histologic variants of LM tend to be misdiagnosed as LMS. Furthermore, the low incidence of LMS has been preventing elucidating its causal mechanisms and developing effective diagnoses and treatments. Therefore, development of molecular diagnosis as an alternative or confirmatory means helps diagnosing LMS more accurately. We adopted omics-based technologies to identify genome-wide features to distinguish LMS from LM, and revealed that copy-number, gene expression, and DNA methylation profiles successfully distinguished between these tumors. LMS was found to possess features typically observed in malignant solid tumors, such as extensive chromosomal abnormalities, overexpression of cell cycle –related genes, and hypomethylation spreading through large genomic regions as well as frequent hypermethylation at polycomb group target gene and cadherin gene loci. We also identified candidate expression and DNA methylation markers, which will help establishing diagnostic tests using conventional quantitative assays. While the identified omics-signatures and certain markers specific to LMS need to be further validated in larger numbers of LM and LMS samples, our results demonstrate the practical feasibility of establishing a postoperative diagnostic test to distinguish LMS from LM with high accuracy, and also suggest the future possibility of developing preoperative and non-invasive diagnostic methods.
2017-02-09 | GSE68304 | GEO
Project description:MicroRNAs (miRNAs) are small noncoding RNAs that participate in regulation of gene expression. Their role during mammary gland development is still largely unknown. In the present study, we performed a microarray analysis to identify miRNAs associated with high mammogenic potential of bovine mammary gland. We identified 54 miRNAs differing significantly between mammary tissue of dairy (Holstein-Friesian, HF) and beef (Limousine, LM) post-pubertal heifers. Fifty two miRNAs had higher expression in the mammary tissue of LM heifers. Enrichment analyses for targeted genes revealed that the major differences between miRNA expression in the mammary gland of HF vs. LM were associated with regulation of signalling pathways crucial for mammary gland development, such as: TGF-beta, insulin, WNT and inflammatory pathways. Moreover, a number of genes potentially targeted by differentially expressed miRNAs was associated with mammary stem cells’ activity. These data indicate that in dairy cattle high developmental potential of the mammary gland, leading to high milk productivity, not only depends on central neuro-endocrine regulation but also on specific miRNA expression pattern. miRNA profiling of Holstein Freisian (dairy breed) and Limousne heifers (beef breed) mammay glands. Two-condition experiment, LM (test) vs. HF (reference). Total RNA was isolated from quarters of 4 LM and 4 HFmammary glands.
2014-09-15 | E-GEOD-61227 | biostudies-arrayexpress