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$nwbo @alphavestcap dstock07734 Re: Nemesis18 post# 689485 Tuesday, May 07, 2024 3:46:23 PM Post# of 689580 Go Have you checked out all the papers from Dr. Liau which have all the data uploaded to GEO DataSets? Obviously, you haven't. Here is the link of all the papers. Go through each of them before you roll the dice and post nonsense. ncbi.nlm.nih.gov/gds/?term=L… Search results Items: 34 Select item 2002492821. Glioblastoma Molecular Characteristics and Immune Microenvironment Associated with Survival Outcomes in Patients Treated with Dendritic Cell Vaccination (Submitter supplied) Purpose: Autologous tumor lysate-pulsed dendritic cell (DC) vaccination has shown promising long-term survival in a cohort of patients with newly diagnosed glioblastoma. The purpose of this study was to better understand the mechanisms and modulation of the immune microenvironment underlying the clinical efficacy of DC-based vaccine therapy. Experimental Design: We performed bulk RNA sequencing on tumor samples from patients with newly diagnosed glioblastoma obtained prior to treatment with dendritic cell vaccination. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 58 SamplesDownload data: TXT SeriesAccession: GSE249282ID: 200249282 Analyze with GEO2R Select item 2002375812. Dendritic Cell Vaccination in Conjunction with TLR Agonist Polarizes Interferon Immune Responses Associated with Long-term Survival in Malignant Glioma Patients (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 64 SamplesDownload data SeriesAccession: GSE237581ID: 200237581 PubMed Full text in PMC Similar studies Select item 2002375793. Dendritic Cell Vaccination in Conjunction with TLR Agonist Polarizes Interferon Immune Responses Associated with Long-term Survival in Malignant Glioma Patients [scRNA-seq] (Submitter supplied) Autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination is a promising immunotherapy for patients with high grade gliomas, but responses have not been demonstrated in all patients. Pre-clinical studies demonstrate that toll-like receptor (TLR) agonists can enhance the anti-tumor immune response from cancer vaccines. To determine the most effective combination of autologous tumor lysate-pulsed DC vaccination, with or without the adjuvant toll-like receptor (TLR) agonists poly-ICLC or resiquimod, we conducted a randomized, open-label multi-arm Phase 2 clinical trial to evaluate immune responses and survival in 23 patients with newly diagnosed or recurrent WHO Grade III-IV malignant gliomas. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 16 SamplesDownload data: MTX, RDS, TSV SeriesAccession: GSE237579ID: 200237579 PubMed Full text in PMC Similar studies Select item 2002375624. Dendritic Cell Vaccination in Conjunction with TLR Agonist Polarizes Interferon Immune Responses Associated with Long-term Survival in Malignant Glioma Patients [Bulk RNA-seq] (Submitter supplied) Autologous tumor lysate-pulsed dendritic cell (ATL-DC) vaccination is a promising immunotherapy for patients with high grade gliomas, but responses have not been demonstrated in all patients. Pre-clinical studies demonstrate that toll-like receptor (TLR) agonists can enhance the anti-tumor immune response from cancer vaccines. To determine the most effective combination of autologous tumor lysate-pulsed DC vaccination, with or without the adjuvant toll-like receptor (TLR) agonists poly-ICLC or resiquimod, we conducted a randomized, open-label multi-arm Phase 2 clinical trial to evaluate immune responses and survival in 23 patients with newly diagnosed or recurrent WHO Grade III-IV malignant gliomas. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 48 SamplesDownload data: CSV, TXT SeriesAccession: GSE237562ID: 200237562 PubMed Full text in PMC Similar studies Select item 2001937455. Landscape of immune checkpoint blockade-induced immune alterations in the microenvironment of primary and metastatic brain tumors (Submitter supplied) Brain tumors reside in an immune privileged microenvironment where inflammatory processes are heavily regulated. Nevertheless, our recent study showed a significant immune infiltration in recurrent glioblastoma (rGBM) treated with neoadjuvant PD-1 checkpoint blockade therapy. Compared to GBM, the intracranial immunotherapy response of brain metastases (BrM) has been much less studied. Therefore we studied the effect of pre-surgical immune checkpoint blockade (ICB) on the immune compartments of BrM, using multiplex immunofluorescence, mass cytometry and single-cell RNA sequencing. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 18 SamplesDownload data: TXT, ZIP SeriesAccession: GSE193745ID: 200193745 PubMed Full text in PMC Similar studies Select item 2001869326. Transcriptomic characterization of GBM tumor and vascular cells and IBSP on patient-delived gliomasphere culture (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.Organism:Homo sapiensType:Expression profiling by array; Expression profiling by high throughput sequencingPlatforms: GPL16791 GPL570 44 SamplesDownload data: CEL SeriesAccession: GSE186932ID: 200186932 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 2001869317. Effect of IBSP on patient-delived gliomasphere culture [microarray] (Submitter supplied) We aim to examine gene expression changes on patient-derived gliomasphere by IBSP treatmentOrganism:Homo sapiensType:Expression profiling by arrayPlatform: GPL570 12 SamplesDownload data: CEL SeriesAccession: GSE186931ID: 200186931 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 2001869308. Transcriptomic characterization of GBM tumor and vascular cells (Submitter supplied) We aim to profile transcrional regulation of GBP tumor and vascular cells by RNA sequencingOrganism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL16791 32 SamplesDownload data: XLSX SeriesAccession: GSE186930ID: 200186930 PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector Select item 2001547959. Cellular and transcriptional immune responses induced by neoadjuvant PD-1 blockade in glioblastoma patients (Submitter supplied) The differentiation and effector function of tumor infiltrating lymphocytes and macrophages in the tumor microenvironment is critical for productive anti-tumor immune responses, although direct evidence for this remains poorly characterized in brain cancer patients. Using mass cytometry, single-cell RNA sequencing, and quantitative multiplex immunofluorescence, we comprehensively characterized the phenotype and single-cell transcriptome of myeloid cells and T lymphocytes that infiltrated malignant gliomas, and identified how such populations changed following neoadjuvant PD-1 checkpoint blockade in recurrent glioblastoma patients. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 40 SamplesDownload data: RDS, TXT SeriesAccession: GSE154795ID: 200154795 PubMed Full text in PMC Similar studies SRA Run Selector Select item 20016307110. NF1 mutation drives neuronal activity-dependent optic glioma initiation (Submitter supplied) The study investigates the role of NF1 mutation and neuronal activity on the initiation of optic pathway glioma, a type of low-grade glioma. the RNAseq dataset investigates mRNA expression profile of human pilocytic astrocytomas (WHO grade I)Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 44 SamplesDownload data: TXT SeriesAccession: GSE163071ID: 200163071 PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector Select item 20016562411. Dopamine Receptor Antagonists and Radiation Create a Metabolic Vulnerability in Mouse Models of Glioblastoma (Submitter supplied) Glioblastoma is the deadliest brain tumor in adults and the standard-of-care consists of surgery followed by radiation and treatment with temozolomide. Overall survival times for patients suffering from glioblastoma are unacceptably low indicating an unmet need for novel treatment options. Using patient-derived glioblastoma lines and mouse models of glioblastoma we tested the effect of radiation and the dopamine receptor antagonist on glioblastoma self-renewal in vitro and survival in vivo. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 12 SamplesDownload data: TXT SeriesAccession: GSE165624ID: 200165624 PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector Select item 20014635812. The Dopamine Receptor Antagonist TFP Prevents Phenotype Conversion and Improves Survival in Mouse Models of Glioblastoma (Submitter supplied) Glioblastoma is the deadliest adult brain cancer and all patients ultimately succumb to the disease. Radiation therapy (RT) provides survival benefit of 6 months over surgery alone but these results have not improved in decades. We report that radiation induces a glioma-initiating cell phenotype and identified trifluoperazine (TFP) as a compound that interferes with this phenotype conversion. TFP caused loss of radiation-induced Nanog mRNA expression, activation of GSK3 with consecutive post-translational reduction in p-Akt, Sox2 and -catenin protein levels. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL24676 24 SamplesDownload data: TXT SeriesAccession: GSE146358ID: 200146358 PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector Select item 20012181013. Neoadjuvant anti-PD-1 immunotherapy promotes a survival benefit with intratumoral and systemic immune responses in recurrent glioblastoma (Submitter supplied) Glioblastoma is the most common primary malignant brain tumor in adults and associated with poor survival. Standard-of-care chemotherapy and radiation confer a median overall survival of under two years. The Ivy Foundation Early Phase Clinical Trials Consortium conducted a randomized, multi institution clinical trial to evaluate immune responses and survival following neoadjuvant and/or adjuvant therapy with pembrolizumab, a programmed cell death protein 1 (PD-1) monoclonal antibody, in 35 patients with recurrent, surgically resectable glioblastoma. more...Organism:Homo sapiensType:Expression profiling by high throughput sequencingPlatform: GPL21290 29 SamplesDownload data: XLSX SeriesAccession: GSE121810ID: 200121810 PubMed Full text in PMC Similar studies Analyze with GEO2RSRA Run Selector Select item 20011713014. Heterogeneity within the PF-EPN-B subgroup (Submitter supplied) Combined EPIC and 450k analysis across 212 posterior fossa ependymoma's classified as PFB using the Heidelberg Brain Tumour Classifier Methylation profiling across 212 posterior fossa PFB ependymoma's to discern molecular heterogeneityOrganism:Homo sapiensType:Methylation profiling by genome tiling arrayPlatforms: GPL21145 GPL16304 212 SamplesDownload data: IDAT, TXT SeriesAccession: GSE117130ID: 200117130 PubMed Full text in PMC Similar studies Select item 20008521815. DNA methylation and gene expression profiling of primary medulloblastoma samples (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.Organism:Homo sapiensType:Expression profiling by array; Methylation profiling by arrayPlatforms: GPL22286 GPL13534 1526 SamplesDownload data: CEL, IDAT SeriesAccession: GSE85218ID: 200085218 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20008521716. Expression data from primary medulloblastoma samples (Submitter supplied) Affimetrix Human Gene 1.1 ST Array profiling of 763 primary medullobalstoma samples used for identification of Medullobastoma subtypesOrganism:Homo sapiensType:Expression profiling by arrayPlatform: GPL22286 763 SamplesDownload data: CEL, TXT SeriesAccession: GSE85217ID: 200085217 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20008521217. DNA methylation profiling of primary medulloblastoma samples (Submitter supplied) Genome wide DNA metylation of 763 primary medulloblastoma samplesOrganism:Homo sapiensType:Methylation profiling by arrayPlatform: GPL13534 763 SamplesDownload data: IDAT, TXT SeriesAccession: GSE85212ID: 200085212 PubMed Full text in PMC Similar studies Select item 20009899518. Large-scale assessment of the gliomasphere model system (Submitter supplied) Some aspects of the gene expression-based classification method were robust because the gliomasphere cultures retained their classification over many passages, and IDH1 mutant gliomaspheres were all proneural. While gene expression of a subset of gliomasphere cultures was more like the parent tumor than any other tumor, gliomaspheres did not always harbor the same classification as their parent tumor. more...Organism:Homo sapiensType:Expression profiling by arrayPlatform: GPL570 71 SamplesDownload data: CEL SeriesAccession: GSE98995ID: 200098995 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20008329419. caArray_nelso-00262: Gene expression profiling of gliomas strongly predicts survival (Submitter supplied) Migrated from 1.6 id: 1015897590491013 GEDP id: 760 In current clinical practice, histology-based grading of diffuse infiltrative gliomas is the best predictor of patient survival time. Yet histology provides little insight into the underlying biology of gliomas and is limited in its ability to identify and guide new molecularly targeted therapies. We have performed large-scale gene expression analysis using the Affymetrix HG U133 oligonucleotide arrays on 85 diffuse infiltrating gliomas of all histologic types to assess whether a gene expression-based, histology-independent classifier is predictive of survival and to determine whether gene expression signatures provide insight into the biology of gliomas. more...Organism:Homo sapiensType:Expression profiling by arrayPlatforms: GPL97 GPL96 170 SamplesDownload data: CEL, CHP, TXT SeriesAccession: GSE83294ID: 200083294 PubMed Similar studies Select item 20006802920. Glioblastoma stem cell (GSC) clones survived 500uM Temozolomide (TMZ) treatment (Submitter supplied) Comparison of parental GSC (GSC-parental) with treatment resistant GSC clones survived 500uM TMZ treatment (GSC-500uM TMZ) We used microarrays to identify defense profiles of GSC-500uM TMZOrganism:Homo sapiensType:Expression profiling by arrayPlatform: GPL570 12 SamplesDownload data: CEL SeriesAccession: GSE68029ID: 200068029 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20004653121. Expression data from glioblastoma stem cell clones (GSC) (Submitter supplied) Comparison of treatment sensitive GSC clones (TSGC) with treatment resistant GSC clones (TRGC). We used microarrays to identify molecular signatures of TRGC (upregulated genes).Organism:Homo sapiensType:Expression profiling by arrayPlatform: GPL570 12 SamplesDownload data: CEL, DCP SeriesAccession: GSE46531ID: 200046531 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20003738522. Subgroup specific somatic copy number aberrations in the medulloblastoma genome (Submitter supplied) Medulloblastoma, the most common malignant pediatric brain tumour is currently treated with non-specific cytotoxic therapies including surgery, whole brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, prior attempts to identify targets for therapy have been underpowered due to small samples sizes. more...Organism:Homo sapiensType:Expression profiling by array; Genome variation profiling by SNP array; SNP genotyping by SNP arrayPlatforms: GPL6801 GPL11532 1382 SamplesDownload data: CEL, CHP SeriesAccession: GSE37385ID: 200037385 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20003738423. Subgroup specific somatic copy number aberrations in the medulloblastoma genome [gDNA] (Submitter supplied) Affymetrix SNP6 profiling of 1087 medulloblastoma samples and 10 medulloblastoma cell lines.Organism:Homo sapiensType:SNP genotyping by SNP array; Genome variation profiling by SNP arrayPlatform: GPL6801 1097 SamplesDownload data: CEL, CHP, TXT SeriesAccession: GSE37384ID: 200037384 PubMed Full text in PMC Similar studies Select item 20003738224. Subgroup specific somatic copy number aberrations in the medulloblastoma genome [mRNA] (Submitter supplied) Affymetrix Human Gene 1.1 ST Array profiling of 285 primary medulloblastoma samples.Organism:Homo sapiensType:Expression profiling by arrayPlatform: GPL11532 285 SamplesDownload data: CEL SeriesAccession: GSE37382ID: 200037382 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20002827125. Isocitrate dehydrogenase 1 (IDH1) mutant gliomas demonstrate a distinct global CpG island methylation profile compared to IDH1 wildtype gliomas using MRSE (Submitter supplied) In order to identify other molecular aberrations that may cooperate with IDH1R132MUT in gliomagenesis, we performed CpG-island methylation profiling analysis using MSRE (Tran et al. Front. Neurosci. 3:57. Doi: 10.3389/neuro.15.005.2009) on a subset of IDH1R132MUT and IDH1R132WT GBMs and found a distinct pattern of CpG island hypermethylation that was detected in all GBMs and lower grade gliomas with IDH1R132MUT. more...Organism:Homo sapiensType:Methylation profiling by genome tiling arrayPlatform: GPL13349 40 SamplesDownload data: TXT SeriesAccession: GSE28271ID: 200028271 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20002244326. Expression data for naïve IL-2 and IL-12 primed Pmel-1 CD8 T-cells (Submitter supplied) The expansion, trafficking and functional effectiveness of adoptively transferred CD8 T-cells play a critical role in mediating effective anti-tumor immunity. However, the mechanisms which program the highly proliferative and functional state of CD8 T-cells are not completely understood. We hypothesized that IL-12, a cytokine commonly induced by TLR activation, could enhance T-cell priming by altering responsiveness to antigen and cytokines. more...Organism:Mus musculusType:Expression profiling by arrayPlatform: GPL6246 6 SamplesDownload data: CEL SeriesAccession: GSE22443ID: 200022443 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20001380827. Bead-based kinase phosphorylation profiling identifies SRC as a therapeutic target in glioblastoma (Submitter supplied) Here we describe a bead-based method capable of profiling tyrosine kinase phosphorylations in a multiplexed, high-throughput and low-cost manner. This approach allows for the discovery of tyrosine kinase-activating events, even when the DNA sequence is wild-type. In an effort to pilot the establishment of a tyrosine kinase activation catalog, we profiled tyrosine phosphorylation levels of 62 tyrosine kinases in 130 human cancer lines, and followed-up on the frequent SRC phosphorylation in glioblastoma. more...Organism:Homo sapiensType:Protein profiling by protein arrayPlatform: GPL7696 130 SamplesDownload data: CSV SeriesAccession: GSE13808ID: 200013808 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20001304128. Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age (Submitter supplied) Background: Glioblastomas are the most common primary brain tumour in adults. While the prognosis for patients is poor, gene expression profiling has detected signatures that can sub-classify GBMs relative to histopathology and clinical variables. One category of GBM defined by a gene expression signature is termed ProNeural (PN), and has substantially longer patient survival relative to other gene expression-based subtypes of GBMs. more...Organism:Homo sapiensType:Expression profiling by arrayPlatforms: GPL570 GPL96 GPL8300 267 SamplesDownload data: CEL SeriesAccession: GSE13041ID: 200013041 PubMed Full text in PMC Similar studies Analyze with GEO2R Select item 20000510729. Distinct Transcription Profiles of Primary and Secondary Glioblastomas (Submitter supplied) Gene expression data of primary and secondary glioblastoma subgroups. Keywords: glioblastoma, transcription profilesOrganism:Homo sapiensType:Expression profiling by arrayPlatform: GPL96 83 SamplesDownload data SeriesAccession: GSE5107ID: 200005107 PubMed Similar studies Analyze with GEO2R Select item 20000508230. SNP Analysis of Primary Glioblastoma Cell Lines (Submitter supplied) Genomic abnormalities that are associated with mesecnhmal phenotype of GBM were detected in glioblastoma cell lines. Keywords: SNP array analysis of glioblastome cell lines.Organism:Homo sapiensType:Genome variation profiling by SNP array; SNP genotyping by SNP arrayPlatform: GPL1266 5 SamplesDownload data SeriesAccession: GSE5082ID: 200005082 PubMed Similar studies Select item 20000441231. freij-affy-human-91666 (Submitter supplied) Diffuse infiltrating gliomas are the most common primary brain malignancy found in adults, and Glioblastoma multiforme, the highest grade glioma, is associated with a median survival of 7 months. Transcriptional profiling has been applied to 85 gliomas from 74 patients to elucidate glioma biology, prognosticate survival, and define tumor sub-classes. These studies reveal that transcriptional profiling of gliomas is more accurate at predicting survival than traditional pathologic grading, and that gliomas characteristically express coordinately regulated genes of one of four molecular signatures: neurogenesis, synaptic transmission, mitotic, or extra-cellular matrix. more...Organism:Homo sapiensType:Expression profiling by arrayDatasets: GDS1975 GDS1976 Platforms: GPL96 GPL97 170 SamplesDownload data: CEL, TXT SeriesAccession: GSE4412ID: 200004412 PubMed Similar studies Analyze with GEO2R Select item 197632. 📷 Gliomas of grades III and IV (HG-U133B) Analysis of grades III and IV gliomas of various histologic types. Results used to develop a gene-expression based, histology independent-classification scheme, and provide insight into the biology of gliomas.Organism:Homo sapiensType:Expression profiling by array, count, 4 cell type, 2 disease state setsPlatform: GPL97 Series: GSE441285 SamplesDownload data: CEL DataSetAccession: GDS1976ID: 1976 PubMed Similar studies GEO Profiles Analyze DataSet Select item 197533. 📷 Gliomas of grades III and IV (HG-U133A) Analysis of grades III and IV gliomas of various histologic types. Results used to develop a gene-expression based, histology independent-classification scheme, and provide insight into the biology of gliomas.Organism:Homo sapiensType:Expression profiling by array, count, 4 cell type, 2 disease state setsPlatform: GPL96 Series: GSE441285 SamplesDownload data: CEL DataSetAccession: GDS1975ID: 1975 PubMed Similar studies GEO Profiles Analyze DataSet Select item 10000769634. Luminex Kinase Phosphorylation Immunosandwich Assay (Submitter supplied) Individual bead-type of Luminex xMAP microspheres (Luminex Corporation, Austin, TX) were coupled separately to capture antibodies against total tyrosine kinases using the following procedure. 100µl Microspheres were washed with 100 µl ddH2O and resuspended in 80 µl 100mM NaH2PO4 pH 6.2. 10 µl 25mg/ml Sulfo-NHS (Pierce) and 10 µl 25mg/ml EDC (Pierce) were added and incubated at 25°C for 20min while shaking to activate the microspheres. more...Organism:Homo sapiens1 Series130 SamplesDownload data

Accuracy benchmark of the GeneMind GenoLab M sequencing platform for WGS and WES analysis. #NGS #SequencingPlatform #SequencingBenchmarking #GeneMind #BMCgenomics bmcgenomics.biomedcentral.co…

Most existing #transcriptome analysis tools are limited to data from a single #sequencingplatform and only several of them could handle more than one analysis module, which are far from enough to meet the requirements of users. @ChinaScience rna-seqblog.com/rna-combine-…