‘Tepidibacillus infernus’
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ABSTRACT:
PROVIDER: PRJEB12870 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Tepidibacillus infernus strain:MBL-TLP Genome sequencing and assembly
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Project description:We explored the mechanism by which TLP affects DNA damage response. We performed mRNA-seq analysis of non-treated and etoposide-treated samples in control and TLP-knockdown cells. We show that TLP is critical for global transcriptional repression after double-strand DNA breaks (DSBs).
2018-10-03 | GSE120734 | GEO
Project description:modENCODE_submission_3216 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP321(official name : TLP-1 genotype : unc119(ed3);wgIs321(tlp-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The spatio-temporal expression pattern of TLP-1::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the TLP-1 transcription factor. made_by : Bob Waterston's lab from UW ); Developmental Stage: fed L1; Genotype: unc119(ed3);wgIs321(tlp-1::TY1 EGFP FLAG;unc119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage fed L1; Target gene tlp-1; Strain OP321(official name : TLP-1 genotype : unc119(ed3);wgIs321(tlp-1::TY1 EGFP FLAG;unc119) outcross : 0 mutagen : None tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The spatio-temporal expression pattern of TLP-1::EGFP fusion protein was examined through in vivo microscopy. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the TLP-1 transcription factor. made_by : Bob Waterston's lab from UW ); temp (temperature) 20 degree celsius
2011-05-24 | E-GEOD-29462 | biostudies-arrayexpress
Project description:Stress constantly challenges plant adaptation to the environment. Of all stress types, arsenic was a major threat during the early evolution of plants. The most prevalent chemical form of arsenic is arsenate, whose similarity to phosphate renders it easily incorporated into cells via the phosphate transporters. Here we found that arsenate stress provokes a notable transposon burst in plants, in coordination with arsenate/phosphate transporter repression, which immediately restricts arsenate uptake. This repression was accompanied by delocalization of the phosphate transporter from the plasma membrane. When arsenate was removed, the system rapidly restored transcriptional expression and membrane localization of the transporter. We identify WRKY6 as an arsenate-responsive transcription factor that mediates arsenate/phosphate transporter gene expression and restricts arsenate-induced transposon activation. Plants therefore have a dual WRKY-dependent signaling mechanism that modulates arsenate uptake and transposon expression, providing a coordinated strategy for arsenate tolerance and transposon gene silencing.
2014-04-25 | GSE49037 | GEO
Project description:Cerebrospinal fluid (CSF) plays an important role in brain tumours, including medulloblastoma (MBL). CSF proteomics studies have mainly focused on extracellular vesicle (EV) proteins rather than the total CSF proteome. Recent advancements in mass spectrometry systems and �쁎mics�� data analysis methods enable unbiased, high proteome depth research. We conducted proteomic profiling of the total CSF in MBL patients with the purpose of finding a potential diagnostic biomarker for MBL. Methods CSF samples from patients with MBL (n=31) and hydrocephalus (HC, control, n=19) were analysed using liquid chromatography-tandem mass spectrometry (LC�묺S/MS). Enrichment analysis of canonical pathways and differentially expressed proteins (DEPs) was performed. Feature selection of the proteins was conducted using the analysis of variance F value and fast correlation-based filter methods. The selected proteins were validated through ELISA and EV characterization using ExoView systems. Results We quantified 1,112 proteins per CSF sample. We further investigated 273 DEPs extracted from a comparison of MBL and HC. Hierarchical clustering of DEPs between MBL and HC clearly showed classification into two groups. Feature selection identified four elevated soluble proteins (SPTBN1, HSP90AA1, TKT, and NME1-NME2) in MBL CSF. Validation with ELISA confirmed that TKT was significantly elevated in MBL compared to HC, as well as in Group 4 MBL and leptomeningeal seeding (LMS). Additionally, TKT-positive EVs were significantly enriched in MBL CSF compared to HC CSF and correlated with the burden of LMS. Conclusions Our results provide insights into the proteomics data of the total CSF of MBL patients. Furthermore, we identified the significance of TKT within the total CSF and its presence within circulating EVs in the CSF. We suggest that TKT may serve as a biomarker for MBL, particularly for the diagnosis of LMS.
2024-08-29 | PXD045982 | Pride