Name: Proteomic data on the biodegradation of doxycycline by Chryseobacterium sp. WX1
Keywords: Chryseobacterium

OmicsDI

Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteomic data on the biodegradation of doxycycline by Chryseobacterium sp. WX1

ABSTRACT: In this study, we isolated a potent doxycycline-degrading bacterium, Chryseobacterium sp. WX1, from environmental samples. To elucidate the molecular mechanisms underlying doxycycline degradation by strain WX1, we assessed and interpreted the proteomic profiles of Chryseobacterium sp. WX1 under conditions both with and without doxycycline exposure.

INSTRUMENT(S): Orbitrap Exploris 480

ORGANISM(S): Chryseobacterium Sp. P567

TISSUE(S): Cell Culture

SUBMITTER: Xiuli Chen

LAB HEAD: Shuguang Xie

PROVIDER: PXD045182 | Pride | 2023-09-07

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

Analysis of differential gene expression in the degradation of doxycycline by Chryseobacterium sp. WX1

Project description:We isolated an efficient doxycycline degrading strain Chryseobacterium sp. WX1. To investigate gene expression patterns during doxycyclinedegradation by strain WX1, we conducted a comparative transcriptomic analysis using cultures of strain WX1 with and without doxycycline addition. The RNA-Seq data revealed that 90.44-96.56% of the reads mapped to the genome of Chryseobacterium sp. WX1 across all samples. Differentially expressed genes (DEGs) analysis (|log2FC| >2; p < 0.01) showed that 693 genes were significantly up-regulated and 592 genes were significantly down-regulated.

2023-09-12 | GSE242785 | GEO

Transcription profiling of mouse embryonic stem cells with a doxycycline-inducible Xist cDNA transgene introduced into chromosome 17

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 17 at approximately 71.24Mb (NCBI Build m36). Insertion of the transgene was heterozygous, so only one copy of chromosome 17 carried the transgene, and the other chromosome 17 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the heterozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline. As background control, total RNA was also prepared from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). The total RNA was then used to make labelled cRNA, which was hybridised to an Affymetrix GeneChip Mouse Genome 430 2.0 array.

2010-05-10 | E-MEXP-2087 | biostudies-arrayexpress

Transcription profiling of mouse embryonic stem cells with a doxycycline-inducible Xist cDNA transgene introduced into chromosome 3

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 3 at approximately 99.79Mb (NCBI Build m36). Insertion of the transgene was homozygous, so only one copy of chromosome 3 carried the transgene, and the other chromosome 3 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the homozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline for three days. As background control, total RNA was also extracted from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). cRNA was labelled from the total RNAs, and then hybridised to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

2010-05-10 | E-MEXP-2086 | biostudies-arrayexpress

Differentiating i-Mixl1 mESCs cultured in the presence or absence of Doxycycline

Project description:We profiled gene expression changes in differentiating i-Mixl1 ES cells(Willey, Ayuso-Sacido et al., 2006, Blood 107(8): 3122-3130) cultured in the presence or absence of Doxycycline (DOX, 0.1 ug/ml, 3 replicates per treatment/time point). Total RNA was isolated from EBs harvested at day 2, 3 and 4 (DOX added 1 day after plating of ES cells). RNA (1 ug) was subjected to one round of linear amplification (RiboAmp System) to yield 10 ug of RNA. The RNA was indirectly labeled using amino allyl-dUTP('t Hoen, de Kort et al., 2003, Nucleic Acids Res. 31: e20), then conjugated with Cy3 or Cy5. The labeled RNAs were used to screen a 15K mouse developmental cDNA microarray(Tanaka, Jaradat et al., 2000, Proc. Natl. Acad. Sci. U.S.A. 97: 9127-9132). Pairwise analysis of hybridization results for EBs cultured with or without DOX was performed for samples harvested on each day. Spotfire(R) software was used for data management and filtering. Gene expression ratios were normalized after filtering the data to remove low-intensity and poor quality spots. Data obtained for replicate samples were in excellent agreement. Six experiments total: three time points (day 2, day 3, day 4); for each time point mRNA was collected in the presence or absence of Doxycycline. Three biological replicas were collected for each of the six experiments

2015-09-01 | E-GEOD-40703 | biostudies-arrayexpress

Transcription profiling of mouse embyronic stem cells expressing the doxycycline-inducible Xist cDNA transgene inserted into chromosome 12 to study of Xist RNA mediated silencing

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 12 at approximately 110Mb (NCBI build m36). Insertion of the transgene was heterozygous, so only one copy of chromosome 12 carried the transgene, and the other chromosome 12 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the heterozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from differentiated ES cells treated with doxycycline. As background control, total RNA was also prepared from uninduced, differentiated ES cells (cultured in parallel to doxycycline-treated cells). The total RNA was then used to make labelled cRNA, which was hybridised to an Affymetrix GeneChip Mouse Genome 430 2.0 array.

2010-05-10 | E-MEXP-2088 | biostudies-arrayexpress

MicroRNA profiling of mouse samples untreated and doxycycline treated CC10-IL13 animals

Project description:The aim of this experiment is to determine microRNAs that are diffferentially regulated in allergic airway inflammation. MicroRNA expression profile between untreated and doxycycline treated CC10-IL13 bitransgenic mice

2009-04-15 | E-MEXP-1992 | biostudies-arrayexpress

Effect of doxycycline treatment on germ-free mice

Project description:To characterize the mitochondrial stress response induced by Doxycycline in vivo in liver and kidneys, we administered doxycycline (Dox) at 500 mg/kg/day (mpkd) in the drinking water to 9 weeks-old germ-free C57BL/6J mice for 16 days, hence eliminating the potential confounding impacts of Doxycycline on the microbiome.

2022-09-14 | GSE202754 | GEO

Proteomic data on the biodegradation of tetracycline by Sphingobacterium sp. WM1

Project description:We isolated a strain that efficiently degrades tetracycline and compared its proteomic data in the presence and absence of tetracycline to analyze the molecular mechanism of tetracycline biodegradation

2023-09-07 | PXD042996 | Pride

Phase II Trial of Doxycycline with Radiotherapy for Rectal Cancer

Project description:Interventions: Doxycycline is a broad-spectrum antibiotic, which prevents the binding of amino-acyltRNA to the messenger RNA-30S ribosomal subunit, preventing polyribosome formation. It is approved in New Zealand for the treatment of chronic prostatitis, sinusitis, syphilis, pelvic inflammatory disease, malaria, recurrent aphthous ulceration, and acne vulgaris. Doxycycline primarily exerts it’s antimicrobial action by bacteriostasis. It also has antinflammatory effects. Doxycycline will be administered as two 100mg tablets orally each morning, starting two days prior to the first dose of short-course radiotherapy (SCRT), until one day prior to surgery for rectal cancer. Surgery will be performed within three weeks of starting radiotherapy treatment. The duration of doxycycline will be between 12 and 23 days, and will be determined by each participant s individual treatment schedule. Adherence will be assessed through a combination of a patient diary, and count of the number of tablets remaining in the drug container on the patients admission for rectal cancer surgery. Primary outcome(s): Difference in the mean immunohistochemistry (IHC) H-scores for CD133 in resected tumours between the doxycycline and control groups.[Based on rectal cancers surgically resected within 3 weeks of radiotherapy.] Study Design: Purpose: Treatment; Allocation: Non-randomised trial; Masking: Open (masking not used);Type of endpoint: Safety/efficacy

| 2471032 | ecrin-mdr-crc

Efficacy and Safety of the Prophylactic Use of Doxycycline +/- Vitamin K Cream

Project description:The aim of this Phase 2, two-arm, randomized, double blind placebo controlled study is to evaluate the efficacy of combination therapy of doxycycline and Vitamin K1 compared to doxycycline plus placebo for the prevention of acne-like skin rash in mCRC patients receiving first line cetuximab treatment.

| 2106044 | ecrin-mdr-crc

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data