RNAseq of combined LUAD and SCLC tumors to look at gene expression changes
Ontology highlight
ABSTRACT: For in-depth characterization of neuroendocrine transformation, we analyzed clinical specimens consisting of combined lung adenocarcinoma (LUAD)/small cell lung carcinoma (SCLC) histology exhibiting clear spatial separation. Microdissection was performed for RNA sequencing.
Project description:Total RNA-seq of blasts derived 100 adult T-ALL cases, 211 AML cases and 13 mixed myeloid/lymphoid leukemias with CpG Island Methylator Phenotype (CIMP). In addition, CD34+ HSPCs derived from 9 healthy donors are used as a control. Due to patient confidentiality considerations, the raw data files for this dataset have been deposited to the EGA controlled-access archive under the accession numbers EGAS00001007094 (study); EGAD00001011054, EGAD00001007646, EGAD00001007581 (datasets).
Project description:We investigated whether GATA2 enhancer-driven transcription of EVI1 in inv(3)/t(3;3) is reversible in leukemia cells. In primary inv(3)/t(3;3) AML, immature CD34+CD15- cells can be discriminated from more mature CD34-CD15- and CD34-CD15+ cells. Besides, we also investigated the effect of deleting a MYB binding site on these cells using CRISPR/Cas9.
Project description:MicroRNAs are important cellular components and their dysfunctions are associated with various disease.Small-cell lung cancer (SCLC) is an aggressive disease with a poor prognosis, but little is know about the underlying machinery that leads to rapid tumor growth and early metastases.In this study, clinical outcome prediction miRNAs were successfully found through expression profiling of a total of 924 miRNA genes in 42 SCLC cases. 42 patients with respectable very limited disease (training set) were enrolled. All the patients underwent surgical resection followed by adjuvant chemotherapy according to the standard of care. Total RNA was extracted from formalin-fixed paraffin-embedded (FFPE)specimens, low molecular weight RNA was seperate and labeled , and then hybridized to capitalbio V3 biochip representing about 924 microRNA . three chip were test in each group, and the procedure was repeated twice.
Project description:Proteomic analysis of differentially expressed proteins in MDA-MB-231 and MCF-10A cell lines when miR-200c and miR-203 were transiently expressed or inhibited, respectively.
Project description:The study aimed to investigate the biological significance and role of the SNAT8 gene in retinal physiology and biological processes.
Project description:RNA capture-sequencing analysis was carried out to study the usage of ESR1 exons and transcripts in different breast cancer models, including both ERα(+) and ERα(-) cell lines. Total RNA was extracted and processed for the analysis.
Project description:We have isolated Circulating Tumor Cells from four Small Cell Lung Cancer Patients at diagnosis and relapse using a two-step method developed in the laboratory. Subsequently, Whole-Exome sequencing was performed on these samples as well as on the corresponding biopsies.
Project description:In order to identify new regulators of the phosphate (Pi) starvation signaling pathway in plants, we analyzed variation in the abundance of nuclear-enriched nuclear proteins isolated from Arabidopsis roots that depends on Pi supply. We used 2-D Fluorescence Difference Gel Electrophoresis and MALDI-TOF/TOF techniques for nuclear proteome separation, visualization and relative protein abundance quantification and identification. Pi-controlled proteins identified in our analysis included components of the chromatin remodeling, DNA replication, and mRNA splicing machineries. In addition, by combining Pi starvation conditions with proteasome inhibitor treatments, we characterized the role of the ubiquitin- (Ub)-proteasome system (UPS), a major mechanism for targeted protein degradation in eukaryotes, in the control of the stability of Pi-responsive proteins. Among Pi-responsive proteins, the histone chaperone NAP1;2 was selected for further characterization, and was shown to display differential nucleo-cytoplasmic accumulation in response to Pi deprivation. We also found that mutants affecting three members of the NAP1 family accumulate lower Pi levels and display reduced expression of Pi starvation-inducible genes, reflecting a regulatory role for these chromatin-remodelling proteins in Pi homeostasis.
Project description:We report that the phytoestrogen genistein acts as a tissue-specific androgen receptor modulator in mouse using a novel androgen reporter mouse line and gene expression profiling. Genistein is a partial androgen agonist/antagonist in prostate, brain, and testis but not in skeletal muscle or lung. Gene expression profiling has been done from prostates of intact and castrated male mice treated with genistein or vehicle. Gene expression profiling was also done from prostates of estradiol-treated intact male mice. Gene expression profiling from prostates of castrated and intact male mice after 5-day genistein- or vehicle-treatment or after 4-day estradiol- or vehicle-treatment.
Project description:This SuperSeries is composed of the following subset Series: GSE25273: Array Comparative Genomic Hybridization of Pancreatic Xenografts and Cell Lines GSE26088: Expression Profiling of Pancreatic Xenografts and Cell Lines Refer to individual Series