RNAseq of GBM tumors with SAT1 knockout
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina NovaSeq 6000
ORGANISM(S): Mus musculus
SUBMITTER: Scott Welford
PROVIDER: E-MTAB-14918 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Analyzing brain region differences for postmortem Alzheimer's disease tissues.
2024-06-30 | E-MTAB-14167 | biostudies-arrayexpress
Project description:Cognitively normal brains are compared to sporadic AD and Down syndrome brains with AD for comparison of two different forms of Alzheimer's disease
2024-06-30 | E-MTAB-14179 | biostudies-arrayexpress
Project description:Clinical proteomics on solid tissue samples from human tumour biopsies present multiple challenges. These include limited sample availability, reducing endogenous protease activity and challenges with efficiently solubilising and digesting proteins for high throughput mass spectrometry while achieving comprehensive proteome coverage. Protocols for cancer biopsy proteomics involves three sample preparation steps: tissue washing, lysis and digestion, followed by peptide clean-up by SPE. Our team have reported improvements in all three steps that greatly reduce processing time, enabling greater automation and higher sample throughput. Our aim was to develop a universal protocol for tissue sample preparation that is quick and simple while improving protein solubilization, proteome coverage and reproducibility. Sample preparation with small (<2 mg) biopsies pose additional limitations including the risk of sample loss and introducing variability with multiple reagent additions steps. We now report a one-pot method called heat and beat (HnB). By identifying the limitations and challenges of the existing protocols, we were able to develop a new protocol with fewer steps by achieving lysis, reduction, alkylation and digestion in essentially a single step which was preceded by a 7 min sample heat treatment step. This was achieved by several changes to the existing protocol including the combined use of a beadbeater for tissue homogenisation followed by pressure cycling technology (PCT) using a Barocycler to further lyse and digest the sample. The procedure requires 38 minutes and was tested on 6 tissue types, across three tissue embedding techniques, fresh frozen, OCT embedded (FF-OCT), and FFPE. Our results show that HnB is an efficient new one-pot procedure. The protocol significantly reduced endogenous protease activity, improves peptide yield by up to 3-fold and delivers digestion efficiency of 85-90% from each sample source. We obtained an increase in the number of proteins identified of up to two-fold while reducing variability and processing time.
2025-03-26 | PXD045405 | Pride
Project description:Identification of strigolactone-dependent genes in barley. Comparison of two organs (shoot and root) allowed to identify tissue specific genes remains under control of strigolactones in barley
2024-07-26 | E-MTAB-13641 | biostudies-arrayexpress
Project description:Tissue samples from human induced pluripotent stem cell-derived intestinal tissue (iPSC-derived intestinal progenitors seeded onto collagen hydrogels) which were transplanted subcutaneously in mice. Mice were sacrificed and tissues were collected after 2, 3 or 4 weeks following engraftment. The tissues were sectioned onto slides and then profiled using NanoString GeoMX DSP (cancer transcriptome atlas). Normal human colon tissue was also profiled as a reference. In both cases, slides were stained for nuclei and cytokeratin. ROIs were selected from in vivo tissue to represent the entire tissue present. For colon reference tissue, crypt apices and bases were selected. Automated segmentation of each ROI using cytokeratin status (positive / negative) was also performed. Gene expression of all genes was evaluated to determine the most differentially expressed (for reference data). These genes and other intestinal genes were specifically investigated further on in vivo samples to ascertain areas of similarity to adult colon and furthermore to demonstrate maturation across timepoints.
2025-02-05 | E-MTAB-13834 | biostudies-arrayexpress
Project description:Glioblastoma multiforme (GBM), the most advanced form of a large subset of brain tumors collectively known as glioma, is the most aggressive and invasive type of brain tumor. Patients usually experience a median survival range of 9 to 12 months. GBMs are extremely difficult to manage because of the tumor cellsâ tendency to migrate and pervade into adjacent tissues. Surgical resection of GBMs generally only slows disease progression because any remaining tumor cells proceed to migrate through brain tissues and reform a new tumor mass. It is hypothesized that the invasive phenotype of these tumor cells may be attributable to unique gene expression. Stationary core and invasive rim tumor cells were collected separately by laser capture microdissection (LCM) from 19 biopsy samples. Identification of differentially expressed genes in the tumor core and invasive rim can give valuable insight to the genes and pathways potentially involved with the invasive phenotype. This information can then be used to generate possible biomarkers, diagnostic markers, or drug targets. Human glioblastoma tumor samples were obtained from patients who underwent primary therapeutic brain tumor resection. All specimens were collected and submitted to the study under institutional review board approved protocols. None of the patients had been subjected to chemotherapy or radiotherapy prior to resection, in order to avoid genetic signatures that are due to exposure to alkylating agents and/or ionizing radiation. All specimens were verified as GBMs by a neuropathologist. Tumors are embedded in OCT, then sectioned in a cryostat at -20C, to a thickness of 8-10 um and placed onto HistoGene slides. Sections to be microdissected are removed from the -80C fixed and stained with an abbreviated Hematoxylin and Eosin protocol. Two thousand tumor core and invasive cells are dissected onto separate caps using the PixCell II instrument using CapSure⢠Macro LCM Caps. The CapSure⢠Macro LCM Caps LCM 0211 should be used with the AutoPix instrument. Cells in the tumor core are identified by nuclear atypia and size and captured using the larger spot sizes. Tumor cells immediately adjacent to necrotic areas, cortical areas, cells with small regular nuclei, endothelial and blood cells should be avoided. Individual white matter invading GBM cells can be identified by means of their nuclear atypia and heteropyknotic staining, which is consistent with that of the cells within the tumor core. They should be microdissected using the 7.5 um laser spot size and the initial power settings recommended by the PixCell II manual. After microdissection all harvested material should immediately be lysed on the cap by applying the lysis buffer (XB) from the PicoPure RNA Isolation Kit according to the PicoPure protocol and stored -80C. Cell populations harvested on different caps can be pooled at the time of RNA isolation. RNA integrity is varified by identification of distinct 28S and 18S ribosomal bands with an Agilent Bioanalyzer using the RNA 6000 Nano LabChip kit. Total RNA was isolated from 2000 LCM cells (to ensure at least 500 ng total RNA) using the PicoPure RNA solation Kit, following manufacturers protocol. mRNA is reverse transcribed with the RiboAmp RNA Amplification kit. 500 ng total RNA is amplified with the RiboAmp RNA Amplification kit, following manufacturerâs instructions. The total yield that can be expected falls between 30 and 60 µg copy RNA. The size of the copy RNA should be verified by gel electrophoresis. Approximately 500ng of copy RNA can be separated on a 1% agarose gel in TAE buffer. A smear of amplified material should be seen between 200 and 3000bp. Six µg amplified RNA are labeled in a RT with SuperScriptIII in the presence of dUTP Cy5 utilizing 6 µg random hexamers as primers. Universal reference RNA is amplified one round in the same manner and labeled with Cy3 dUTP. Labeled cDNA is hybridized overnight onto cDNA microarray. Following hybridization, arrays are washed, scanned and quantitated with the Axon GenePix 4000 microarray reader (Axon Instruments). Gene expression results are analyzed using GeneSpring (Silicon Genetics) software. Intensity dependent normalization is applied, where the ratio is reduced to the residual Lowess fit of the intensity versus ratio curve. The measured intensity of each gene is divided by its reference channel (signal from the universal reference RNA) in each sample. When the reference channel is below 10, the data point is considered uninformative. The ratios (sample over reference) for the tumor core experiments and invasive rim experiments are averaged and compared. Genes that are more than two-fold differentially regulated in the majority of the matched core/invasive rim sets are selected.
2010-05-18 | E-GEOD-12689 | biostudies-arrayexpress
Project description:Mice with colonic tumors (chemically induced by AOM/DSS) were treated with Nutlin or control vehicle solution to analyze p53 target gene expression in vivo.
2021-04-20 | E-MTAB-10041 | biostudies-arrayexpress
Project description:Candida spp. represent the third most frequent worldwide cause of infection in Intensive Care Units (ICUs) with a mortality rate of almost 40%. The classes of antifungals currently available include azoles, polyenes, echinocandins, pyrimidine derivatives, and allylamines. However, the therapeutical options for the treatment of candidiasis are drastically reduced by the increasing antifungal resistance. The growing need of a more targeted antifungal therapy is limited by the concern of finding molecules that specifically recognize the microbial cell without damaging the host. Epigenetic writers and erasers have emerged as promising targets in different contexts, including the treatment of fungal infections. In C. albicans, Hst3p, a sirtuin that deacetylates histone H3K56ac, represents an attractive antifungal target as it is essential for the fungus viability and virulence. Although the relevance of such epigenetic regulator is documented for the development of new antifungal therapies, the molecular mechanism behind Hst3p-mediated epigenetic regulation remains unrevealed. Here, we provide the first genome-wide profiling of H3K56ac in C. albicans; H3K56ac enriched regions are associated with Candida sp. pathogenicity. Upon Hst3p inhibition, 447 regions gain H3K56ac. Importantly, these genomic areas contain genes encoding for adhesin proteins, degradative enzymes, and white-opaque switch. Moreover, our RNA-seq analysis revealed 1330 upregulated and 1081 downregulated transcripts upon Hst3p inhibition, and among them, 87 genes whose transcription upregulation correlates well with changes in promoter H3K56 acetylation, including some well-known regulators of phenotypic switching and virulence, confirming that Hst3p is an appealing target for the development of new potential antifungal target.
2023-02-04 | E-MTAB-12167 | biostudies-arrayexpress
Project description:Stressful environmental conditions, including heat stress (HS), are a major limiting factor in crop yield. Understanding the molecular mechanisms of plant stress memory and resilience is important for improving crop yield. We performed a temporal atlas of DNA methylation to reveal the biological pathways and potential functional inter-layer associations affected by HS
2023-03-17 | E-MTAB-12727 | biostudies-arrayexpress
Project description:We performed a quantitative proteome comparison on formalin-fixed paraffin embedded (FFPE) tissue of metastasized and non-metastasized primary prostate cancer (PCa) and on recurrent lymph node metastases. Comparing these three sample groups, we aimed to identify proteins, that might potentially promote/supress tumor progression or metastasis formation. Proteins were quantified label-free. Proteins with interesting biological functions were followed-up by immunohistochemistry.
2017-12-19 | PXD005833 | Pride