Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR13248955_1.fastq.gz | Fastqsanger.gz | |||
| ERR13248955_2.fastq.gz | Fastqsanger.gz | |||
| ERR13245285.fastq.gz | Fastqsanger.gz |
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Project description:Cis bilamellatus genome assembly, icCisBila1, alternate haplotype
| PRJEB105252 | ENA
Project description:As one of the widely-used broad-spectrum anti-cancer drug, ototoxicity occurrence limited the usage of Cisplatin in clinical practice. At the same time, Eleutheroside E are found with kindny and never protection. However, the mechanism of the protection is remained unclear. In this study, 27 C57BL/6J mice were used and divided into Ctrl group with normal Saline injected, Cis and Cis + EE group with injection of Cis and Cis + EE peritoneally for Cisplatin-reduced ototoxicity modelling and intervention, then cochlears were dissected for proteomics. Network pharmacology to predict the target and biological mechanism of Eleutheroside E against cisplatin ototoxicity and Eleutheroside E might play an antagonistic role through the regulation of MAPK and pyrogenic signaling pathway. Compare with Cis group, Cis+EE group mice have a lower threshold value in ABR result and the group shows less cell pyroptosis than Cis group. Morphology results also indicated that Cis+EE group reduced space of spiral ganglion and the vascular structure was relatively clear than the Cis group. In addition, compared with Cis group, mRNA expression of NLRP3, GSDMD, ASC, Caspase-1, IL-1β and IL-18 genes in Cis+EE group decreased. The expression of p-JNK, p-ERK, P-P38, NF-κB P65, Cleaved Caspase-1, GSDMD was decreased, and the expression of IκB was increased. This study demonstrated that Eleutheroside E exerts an antagonistic effect on Cisplatin ototoxicity by down-regulating the activity of MAPK/NF-κB/NLRP3 signaling pathway, reducing the expression level of pyroptosis related proteins and inflammatory factors after cisplatin administration, and then inhibiting pyroptosis.
2023-11-16 | PXD047048 |
Project description:We reported a comprehensive proteogenomics analysis, including whole-genome sequencing, RNA sequencing, and proteomics and phosphoproteomics profiling, of 448 trace-tumor-samples from 190 urothelial bladder neoplasm patients, covering the whole spectrum of disease stages and grades. DNA damage was a key signaling pathway in the progression of carcinoma in situ (CIS) and related to APOBEC signature. Proteogenomic integration analysis indicated the mutation of HRAS regulated mTOR signaling to form urothelial papilloma rather than papillary urothelial cancer (PUC). Glucolipid metabolism increase and lower immune cell infiltration were significantly associated with PUC compared to CIS. Proteomic analysis distinguished the origins of invasive tumors (PUC-derived and CIS-derived), related to distinct clinical prognosis and molecular features. Additionally, loss of RBPMS, associated with CIS-derived tumors, was validated to increase the activity of SMAD-bound JUN and promote metastasis.
2023-08-02 | PXD043775 |
Project description:cis-antisense RNAs (cis-asRNAs) in prokaryotes are more pervasive than originally thought. However, little is known about their expression patterns and functions. Here we determined transcriptomes and proteomes of E. coli at multiple time points in five culture conditions using directional RNA-seq and tandem mass spectrometry. We found that a highly varying portion (27.2%~90.8%) of transcribed genes had cis-asRNAs dependent on growth phases and culture conditions, and that almost all transcribed genes changed their cis-asRNA levels relative to the mRNA level at different growth phases and culture conditions. Intriguingly, the correlation between the protein and mRNA levels of genes is abolished the increasing cis-asRNA levels relative to the mRNA levels, suggesting that cis-asRNAs might directly or indirectly inhibit translation by forming duplexes with mRNAs. All data sets are available for data mining from a unified resource to support further biological discoveries and insights into cis-asRNA-mediated gene expressional regulation.
2022-02-28 | PXD001640 | Pride
Project description:Omics approaches employed to study biological molecules have revolutionized environmental microbiology and elevated our understanding of ecological processes in the biosphere. However, conventional omics applications often lead to the loss of information about macromolecular organization of the molecules within the cellular context. This can be a significant disadvantage since many proteins are functional only as macromolecular complexes in particular structural forms. A great example is bacterial contractile injection system (CIS), a syringe-like protein complex whose function is the translocation of molecules into a target cell to affect its state, often inducing lysis. Since the function of CIS is tightly linked to its intracellular localization, proteomics cannot confidently predict the function of novel uncharacterized CISs in natura. To overcome this challenge, we have developed a cryo-electron tomography workflow as a technique complementing metagenomics and proteomics. Additionally, we developed an immuno-electron microscopy protocol to identify and quantify CIS particles in environmental samples. Using this approach, we discovered a novel bacterial CIS in thermophilic multicellular Chloroflexota bacteria populating hot spring mats worldwide. We found that this system is similar phylogenetically and structurally to a recently described cytoplasmic CIS, which was found in multicellular Streptomyces and has been shown to be involved in cell cycle regulation. Interestingly, using our approaches, we have discovered that Chloroflexota cells produce different numbers of CIS particles depending on the mat micro-niches they occupy. In agreement with this, we observed that CIS was also non-constitutively expressed under laboratory conditions. Motivated by this discovery, we searched and analyzed similar CIS in extremophilic bacteria from other lineages. Overall, we have gained an understanding that bacterial cytoplasmic CIS is an overlooked cellular feature of the extremophilic bacteria, which is potentially involved in the cell fate control or intraspecies interaction within microbial community.
2026-03-23 | PXD071052 | Pride