Project description:Lipidomic LC/MS of neurons and lipid droplets isolated from mouse. Extracted using MTBE and run on an Agilent 1290 Infinity II LC with MS acquisition on an Agilent QToF 6546.
Project description:Metabolic profiling of serum samples were performed on an Agilent 1290 infinity system (Agilent technologies, Santa-Clara, California, USA) coupled to an AB SCIEX Triple TOF 6600 System (AB SCIEX, Framingham, MA, USA) with an electrospray ion (ESI) source in both positive and negative ion modes. There were 30 differential metabolites under positive ion mode and 23 differential metabolites under negative ion mode, respectively.
Project description:Metastasis accounts for almost 90% of breast cancer-related fatalities, making it frequent malignancy and the main reason of tumor mortality globally among women. A key player in breast cancer is the histone demethylase lysine-specific demethylase 1 (LSD1). We used LSD1 knockdown MCF7 and T47D cell exosomes to treat breast cancer cells for greatly increasing the invasion and migration of breast cancer cells for evaluating the impact of LSD1 on breast cancer invasion and migration. miR-1290 expression was downregulated in LSD1 knockdown MCF7 exosomes. Furthermore, miR-1290 could control NAT1 expression by looking through the database of miR-1290 target genes. These data provide fresh insights into the biology of breast cancer therapy by demonstrating how the epigenetic factor LSD1 stimulates the breast cancer cells’ invasion and migration via controlling exosomal miRNA.
Project description:Comparative genomic hybridization analysis for detection of copy number variation for cancer genes in breast cancer mestastatic brain tumors DNA was isolated and analyzed in a two-color experiment using Cancer CGH+SNP 180Kx4 arrays from Agilent and Agilent SureScan system: Cy5-labeled specimen DNA and Cy3-labeled reference Agilent (female) reference DNA
Project description:Strains Achromobacter insuavis and Enterobacter cancerogenus, as well as their co-culture, were grown in LB medium with/without 100 mg/L Cd²⁺ for 48 h. For label‑free proteomics, cells were lysed in urea/thiourea/CHAPS buffer, homogenized, sonicated, and centrifuged. The protein precipitate was analyzed by LC-MS/MS (Agilent 1290‑TripleTOF 5600).
Project description:Purpose: We generated extensive transcriptional and proteomic profiles from a Her2-driven mouse model of breast cancer that closely recapitulates human breast cancer. This report makes these data publicly available in raw and processed forms, as a resource to the community. Importantly, we previously made biospecimens from this same mouse model freely available through a sample repository, so researchers can obtain samples to test biological hypotheses without the need of breeding animals and collecting biospecimens. Experimental design: Twelve datasets are available, encompassing 841 LC-MS/MS experiments (plasma and tissues) and 255 microarray analyses of multiple tissues (thymus, spleen, liver, blood cells, and breast). Cases and controls were rigorously paired to avoid bias. Results: In total, 18,880 unique peptides were identified (PeptideProphet peptide error rate â¤1%), with 3884 and 1659 non-redundant protein groups identified in plasma and tissue datasets, respectively. Sixty-one of these protein groups overlapped between cancer plasma and cancer tissue. Conclusions and clinical relevance: These data are of use for advancing our understanding of cancer biology, for software and quality control tool development, investigations of analytical variation in MS/MS data, and selection of proteotypic peptides for MRM-MS. The availability of these datasets will contribute positively to clinical proteomics. Custom Agilent 44K whole mouse genome expression oligonucleotide microarrays were used to profile breast tumors from three Her2/Neu mice compared to normal breast epithelium from two control mice transgenic for TetO-NeuNT only and littermates of the bitransgenic mice. All samples were laser-capture microdissected and total RNA isolated and amplified prior to hybridization against a reference pool of normal adult mouse tissues.
Project description:In this project we used the strain E. coli BW25113 ΔfrmA::frt (Δ(araD-araB)567, ΔlacZ4787(::rrnB-3), λ-, rph-1, Δ(rhaD-rhaB)568, hsdR514, ΔfrmA(::frt)) from the Keio collection (Baba et al. 2006). The plasmid {pSEVA424_mdh-das} (Low-copy-number, lacIq/Ptrc promoter, RK2 ori, SmR) from Silva-Rocha et al. 2013 was integrated in the strain to express mdh (Methanol dehydrogenase) and das (Dihydroxyacetone synthase) respectively from Acinetobacter gerneri and Pichia angusta. In this experiment, we inoculated 50 mL of M9 minimal medium with 15 mM xylose and with or without 0.15 M methanol, in baffled flasks at 30°C, 150 rpm. At D600=1 and D600=2, 12mL of each culture were centrifuged 1’30 at 14000 rpm before discarding the supernatant and freezing the pellets for 15 sec in liquid nitrogen. RNA extraction were carried out using a RNeasy Midi Kit (Qiagen, Venlo, Netherlands) according to the manufacturer’s protocol and the transcriptomic experiments were run at the GeT-Biopuces Platform (Toulouse, France). Prior to the experiment, the quality of the RNA extracted was analyzed by Nanodrop and Cell Bio Analyser (Agilent Technologies, California, USA). The labelling with Cy3, hybridation on the Agilent chip and wash were carried out accordingly to the Agilent protocol and kits. We used the scanner NimbleGen MS 200 (Roche, Bâle, Suisse) with the following parameters: autogain, 5micros resolution, 532nm scan. The Agilent Feature Extraction software was used to extract the data.