Transcriptomic profiling of formalin-fixed, paraffin-embedded human sarcoma specimens
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Andrew Kelly
PROVIDER: E-GEOD-35852 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:To find how RA signaling modulates HSC development This microarray was performed between E11.5 AA4.1/VEC+CD45- and AA4.1/VEC+CD45+ cells
2013-03-12 | E-GEOD-45020 | biostudies-arrayexpress
Project description:Differential gene expression study comparing choriogonadotropin alpha (Cga) gene deficient and wild type adult mouse pituitary. Thyrotrope hyperplasia and hypertrophy are common responses to primary hypothyroidism. To understand the genetic regulation of these processes, we studied gene expression changes in the pituitaries of Cga-/- mice, which are deficient in the common alpha subunit of TSH, LH and FSH. These mice have thyrotrope hypertrophy and hyperplasia and develop thyrotrope adenoma. We report that cell proliferation is increased, but the expression of most stem cell markers is unchanged. The alpha subunit is required for secretion of the glycoprotein hormone beta subunits, and mutants exhibit elevated expression of many genes involved in the unfolded protein response, consistent with dilation and stress of the endoplasmic reticulum. Mutants have elevated expression of transcription factors that are important in thyrotrope function, such as Gata2 and Isl1, and those that stimulate proliferation, including Nupr1, E2f1 and Etv5. We characterized the expression and function of a novel, over-expressed gene, transcription elongation factor A (SII)-like 5 (Tceal5). Stable expression of Tceal5 in a pituitary progenitor cell line is sufficient to increase cell proliferation. Thus, Tceal5 may act as a proto-oncogene. This study provides a rich resource for comparing pituitary transcriptomes and an analysis of gene expression networks. Total RNA was obtained from 8 week old Cga-deficient and littermate wild type mouse pituitary tissue. Total sample number was 24 as follows: 6 male and 6 female wild types, 6 male and 6 female mutants. Each sample was applied to an individual microarray.
2016-08-05 | E-GEOD-79451 | biostudies-arrayexpress
Project description:Analysis of gene-expression alterations in primitive LT-HSCs as early as 2 days post sex steroid ablation. This study aimed to determine potential intrinsic changes occuring in the LT-HSC population associated with sex steroid ablation (SSA) at a timepoint that preceeded the earliest reported functional hematopoietic enhancements occuring at day 7 post SSA. These results are vital in providing insight into the role of LT-HSCs in initiating SSA-mediated immune regeneration. Total RNA obtained from BM-sorted LT-HSC 2 days after sex steroid ablation compared to sham sex steroid ablation controls.
2015-03-01 | E-GEOD-64841 | biostudies-arrayexpress
Project description:Although majority of the genes linked to pediatric cataract exhibit lens fiber cell-enriched expression, our understanding of gene regulation in these cells is limited to function of just eight transcription factors and largely in the context of crystallins. Here, we identify small Maf transcription factors MafG and MafK as regulators of several non-crystallin human cataract genes in fiber cells and establish their significance to cataract. We applied a bioinformatics tool for cataract gene discovery iSyTE to identify MafG and its co-regulators in the lens, and generated various null-allelic combinations of MafG:MafK mouse mutants for phenotypic and molecular analysis. By age 4-months, MafG-/-:MafK+/- mutants exhibit lens defects that progressively develop into cataract. High-resolution phenotypic characterization of MafG-/-:MafK+/- lens reveals severe defects in fiber cells, while microarrays-based expression profiling identifies 97 differentially regulated genes (DRGs). Integrative analysis of MafG-/-:MafK+/- lens-DRGs with 1) binding-motifs and genomic targets of small Mafs and their regulatory partners, 2) iSyTE lens-expression data, and 3) interactions between DRGs in the String database, unravels a detailed small Maf regulatory network in the lens, several nodes of which are linked to human cataract. This analysis prioritizes 36 highly promising candidates from the original 97 DRGs. Significantly, 8/36 (22%) DRGs are associated with cataracts in human (GSTO1, MGST1, SC4MOL, UCHL1) or mouse (Aldh3a1, Crygf, Hspb1, Pcbd1), suggesting a multifactorial etiology that includes elevation of oxidative stress. These data identify MafG and MafK as new cataract-associated candidates and define their function in regulating largely non-crystallin genes linked to mouse and human cataract. Microarray comparision of lenses from mixed background (129Sv/J, C57BL/6J, and ICR) control (MafG+/-:MafK+/-; no-cataract) and compound (MafG-/-:MafK+/-; cataract) mouse mutants
2015-05-01 | E-GEOD-65500 | biostudies-arrayexpress
Project description:DBC1 KO B cells were either unstimulated, activated with anti-IgM, anti-CD40 of LPS for 4 hours. Genes differentially expressed in DBC1 KO B cells were compared to WT B cells. RNA was collected from unstimulated for stimulated B cells, and gene expression between WT and DBC1 KO B cells were compared
2014-09-04 | E-GEOD-61029 | biostudies-arrayexpress
Project description:Analysis of the genome-wide response of the ER:PRL-HeLa cell line to treatment with estrogen receptor ligands estradiol, 4H-tamoxifen and bisphenol-A. Total RNA obtained from ER:PRL-HeLa cells treated for 4 hours with estradiol, 4H-tamoxifen or bisphenol -A is compared to vehicle treated controls
2011-07-13 | E-GEOD-22941 | biostudies-arrayexpress
Project description:The goal was to examine gene expression after in vivo activation by different vaccine strains of Listeria monocytogenes. Heat killed LM, irradiated LM and live actA- LM were used to immunize mice after transfer of OT-I cells 5x10e5 OT-I-RAG-/- cells transferred to B6 mice, 24hrs later mice immunized; 24hrs later cells sorted on MHC class II-, CD45.1+, CD8+, CD69+ Two arrays were performed per sample for a total of 8 arrays. RAW data file (supplementary file on the Series record) contains the data for each array individually.
2010-06-08 | E-GEOD-20265 | biostudies-arrayexpress
Project description:The effects of Gata4 inhibition on global gene expression in mLTC-1 cells was analysed. Using microarray analysis we identified a set of genes that are downregulated or upregulated following siRNA-mediated silencing of Gata4 in the murine Leydig tumor cell line mLTC-1. Among the downregulated genes were enzymes of the androgen biosynthetic pathway. mLTC-1 cells were transfected with non-targeting (NT) siRNA and Gata4 siRNA respectively. 72h post transfection cells were lysed and RNA was extracted. n=3 of each sample group; control samples are samples 3-6 (mLTC-1 cells treated with non-targeting siRNA)
2015-02-23 | E-GEOD-63320 | biostudies-arrayexpress
Project description:Formalin-fixed paraffin-embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high-definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues, we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas), including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples. A total of 23 test samples were each hybridized with a pooled 46,XX commercial reference (Promega catalog# G1521, Madison, WI). Twenty-two of the test samples included flow-sorted fresh frozen and formalin-fixed paraffin-embedded tumor samples. The tissues included pancreatic adenocarcinomas, breast carcinomas, small cell carcinoma of the ovary, glioblastoma, and bladder carcinoma. The last test sample was a pancreatic adenocarcinoma cell line (A10-74).
2012-12-31 | E-GEOD-40299 | biostudies-arrayexpress
Project description:Analysis of gene expression in explanted peritoneal macrophages from Aoah -/- and Aoah +/+ mice treated with LPS 21 days prior to harvest. Explanted peritoneal machrophages were challenged with LPS or control (PBS). The study seeks to characterize global gene expression in the state of prolonged LPS tolerance induced in mice lacking the LPS-inactivating enzyme Aoah. Groups of 9 C57BL/6 Aoah+/+ or Aoah-/- mice were given i.p. injections of 10 µg E. coli LPS/mouse. Twenty-one days later (when Aoah-/- mice remain tolerant and Aoah+/+ mice have recovered), peritoneal macrophages were harvested and the yields from three mice were pooled to form 3 samples per group (i.e., three samples of Aoah+/+ and Aoah-/- mice, with each sample comprised of peritoneal macrophages from 3 mice). Next day, cells were challenged with LPS or PBS and whole RNA was isolated 2 hours later and used for microarray experiments.
2012-08-17 | E-GEOD-40154 | biostudies-arrayexpress