Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14352168_1.fastq.gz | Fastqsanger.gz | |||
| SRR14352168_2.fastq.gz | Fastqsanger.gz | |||
| SRR14352169_1.fastq.gz | Fastqsanger.gz | |||
| SRR14352169_2.fastq.gz | Fastqsanger.gz | |||
| SRR14352170_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:In addition to germ cell population, testes contain several types of somatic cells, including Sertoli cells, Leydig cells, and peritubular myoid (PTM) cells. PTM cells are a type of smooth muscle-like cells and have contraction ability. To identify a marker of PTM cells, we isolated primary cells and subsequently performed miRNA-Seq of testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3), testicular Sertoli cells (Sertoli_1, Sertoli_2, Sertoli_3), testicular Leydig cells (Leydig_1, Leydig_2, Leydig_3), testicular germ cells (Germ_1, Germ_2, Germ_3), vascular smooth muscle cells (VSMC_1, VSMC_2, VSMC_3), intestinal smooth muscle cells (ISMC_1, ISMC_2, ISMC_3), and tracheal smooth muscle cells (TSMC_1, TSMC_2, TSMC_3) using BGISEQ-500 platform (BGI, China).
2019-01-19 | GSE125302 | GEO
Project description:Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution. Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA. Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states. Examination of Brd and HP1 proteins-binding sites in HEK293 cells.
2012-07-31 | E-GEOD-39579 | biostudies-arrayexpress
Project description:In addition to germ cell population, testes contain several types of somatic cells, including Sertoli cells, Leydig cells, and peritubular myoid (PTM) cells. PTM cells are a type of smooth muscle-like cells and have contraction ability. To identify a marker of PTM cells, we isolated primary cells and subsequently performed RNA-Seq of testicular peritubular myoid cells (PTM_1, PTM_2, PTM_3), testicular Sertoli cells (Sertoli_1, Sertoli_2, Sertoli_3), testicular Leydig cells (Leydig_1, Leydig_2, Leydig_3), testicular germ cells (Germ_1, Germ_2, Germ_3), vascular smooth muscle cells (VSMC_1, VSMC_2, VSMC_3), intestinal smooth muscle cells (ISMC_1, ISMC_2, ISMC_3), and tracheal smooth muscle cells (TSMC_1, TSMC_2, TSMC_3) using BGISEQ-500 platform (BGI, China).
2019-01-19 | GSE125303 | GEO
Project description:Potato response to PTM herbivory.
| PRJEB51839 | ENA
Project description:Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution. Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA. Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states. Comparison of Brd2 and HP1b shRNA knockdown HEK293 cells to control knockdown HEK293 cells.
2012-07-30 | E-GEOD-39580 | biostudies-arrayexpress
Project description:Chryseobacterium marse PTM-20240506 genome sequencing
| PRJNA1224932 | ENA
Project description:B-methylthiolation of the Escherichia coli Ribosomal Protein S12 Regulates Anaerobic Gene Expression. B-methylthiolation is a unique post-translational modification (PTM) that maps to a conserved Asp 88 of the bacterial ribosomal protein S12. This modification is phylogenetically conserved in several bacteria yet has not been identified on other proteins. We use microarrays to delineate the association of prokaryotic ribosomal protein PTM to the regulation of genes.
2010-05-27 | E-GEOD-21551 | biostudies-arrayexpress
Project description:Background: Histone post-translational modifications (PTMs) constitute a branch of epigenetic mechanisms that can control the expression of eukaryotic genes in a heritable manner. Recent studies have identified several PTM-binding proteins containing diverse specialized domains whose recognition of specific PTM sites leads to gene activation or repression. Here, we present a high-throughput proteogenomic platform designed to characterize the nucleosomal make-up of chromatin enriched with a set of histone PTM-binding proteins known as histone PTM readers. We support our findings with gene expression data correlating to PTM distribution. Results: We isolated human mononucleosomes bound by the bromodomain-containing proteins Brd2, Brd3 and Brd4, and by the chromodomain-containing heterochromatin proteins HP1alpha and HP1beta. Histone PTMs were quantified by mass spectrometry (ChIP-qMS), and their associated DNAs were mapped using deep sequencing. Our results reveal that Brd- and HP1-bound nucleosomes are enriched in histone PTMs consistent with actively transcribed euchromatin and silent heterochromatin, respectively. Data collected using RNA-Seq (GSM301568) show that Brd-bound sites correlate with highly expressed genes. In particular, Brd3 and Brd4 are most enriched on nucleosomes located within HOX gene clusters, whose expression is reduced upon Brd4 depletion by shRNA. Conclusions: Proteogenomic mapping of histone PTM readers, alongside the characterization of their local chromatin environments and transcriptional information, should prove useful for determining how histone PTMs are bound by these readers and how they contribute to distinct transcriptional states.
2012-07-31 | GSE39579 | GEO
Project description:Context: Pretibial myxedema (PTM) is a refractory autoimmune dermopathy associated with Graves’ disease. Although metabolic dysregulation has been recognized in thyroid-associated disorders, the metabolic profile and its functional role in PTM remain unclear. Objective: To characterize the metabolic landscape of PTM lesions and explore the contribution of fatty acids to fibroblast dysfunction and inflammation. Methods: We performed untargeted metabolomic profiling of PTM skin lesions and healthy controls using LC-MS and GC-MS, integrated with spatial metabolomics to localize metabolic changes. Functional assays were conducted by stimulating human foreskin fibroblasts (HFFs) with palmitic acid (PA) and oleic acid (OA), followed by RNA sequencing, cytokine assays, and immunohistochemistry. Results: PTM lesions exhibited substantial metabolic reprogramming, including accumulation of fatty acids and elevated tricarboxylic acid cycle intermediates. Spatial metabolomics confirmed pronounced lipid deposition in the dermis, the primary site of PTM pathology. RNA-seq of fibroblasts stimulated with PA and OA revealed enrichment of inflammatory pathways, including IL-17 and NF-κB signaling, and marked upregulation of IL-8 (CXCL8). Fatty acid stimulation induced robust IL-8 secretion, consistent with increased IL-8 expression in PTM lesions. Moreover, PA promoted α-SMA expression in fibroblasts, suggesting induction of myofibroblast differentiation. Conclusions: Our findings demonstrate that dermal fatty acid accumulation in PTM may contribute to fibroblast-mediated inflammation and fibrosis. This study provides novel insights into the metabolic-immunologic interface underlying PTM pathogenesis.
2026-02-01 | GSE317276 | GEO