Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Subclassification of lung adenocarcinoma

ABSTRACT: To elucidate whether or not a subtype of adenocarcinoma with neuroendocrine nature has poor prognosis, we performed gene expression of lung adenocarcinoma profiling by cDNA microarray. adenocarcinoma 154, squamous 10

ORGANISM(S): Homo sapiens

SUBMITTER: T Fujiwara

PROVIDER: E-GEOD-20853 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

ASCL1-coexpression profiling but not single gene expression profiling defines lung adenocarcinomas of neuroendocrine nature with poor prognosis.

Fujiwara Takeshi T Hiramatsu Miyako M Isagawa Takayuki T Ninomiya Hironori H Inamura Kentaro K Ishikawa Shumpei S Ushijima Masaru M Matsuura Masaaki M Jones Michael H MH Shimane Miyuki M Nomura Hitoshi H Ishikawa Yuichi Y Aburatani Hiroyuki H

Lung cancer (Amsterdam, Netherlands) 20110706 1

<h4>Background</h4>Lung adenocarcinoma is heterogeneous regarding histology, etiology and prognosis. Although there have been several attempts to find a subgroup with poor prognosis, it is unclear whether or not adenocarcinoma with neuroendocrine (NE) nature has unfavorable prognosis.<h4>Materials and methods</h4>To elucidate whether a subtype of adenocarcinoma with NE nature has poor prognosis, we performed gene expression profiling by cDNA microarray for 262 Japanese lung cancer and 30 normal ...[more]

PMID: 21737174

Similar Datasets

Transcription profiling of human hematopoietic stem cell like fractions from individuals with the M2 subtype of acute myeloid leukemia

Project description:AC133+ cells were prepared from bone marrow of individuals with acute myeloid leukemia (AML) with M2 subtype. Comparison was made between de novo AML and MDS-associated AML.

2003-10-09 | E-MEXP-25 | biostudies-arrayexpress

Unique microRNA profiles in EGFR-mutated lung adenocarcinomas

Project description:We have examined the microRNA expression in 154 lung adenocarcinoma samples and 20 paired normal lung tissue samples and investigated the microRNA expression to clinical variables, EGFR- and KRAS- mutational status and time to progression. 174 samples are analyzed. 154 from lung adenocarcinoma tumor tissue and 20 from paired normal lung tissue samples. No replicates or control samples included.

2014-03-10 | E-GEOD-48414 | biostudies-arrayexpress

Molecular characterization of Notch1 positive progenitor cells in the developing retina

Project description:The oscillatory expression of Notch signaling in neural progenitors suggests that both repressors and activators of neural fate specification are expressed in the same progenitors. Since Notch1 regulates photoreceptor differentiation and contributes (together with Notch3) to ganglion cell fate specification, we hypothesized that genes encoding photoreceptor and ganglion cell fate activators would be highly expressed in Notch1 receptor-bearing (Notch1+) progenitors, directing these cells to differentiate into photoreceptors or into ganglion cells when Notch1 activity is diminished. To identify these genes, we used microarray analysis to study expression profiles of whole retinas and isolated from them Notch1+ cells at embryonic day 14 (E14) and postnatal day 0 (P0). To isolate Notch1+ cells, we utilized immunomagnetic cell separation. RNA from Notch1+ cells and whole retinas at E14 and P0 was extracted and used for microarray analysis. We processed individual samples that each contained 200,000-500,000 Notch1+ cells. A total of three independent biological replicates in the early stage (E14) of retinal development and four independent biological replicates in the late stage (P0) of retinal development were obtained for comparative profiling of Notch1+ cells and whole retinas.

2015-07-01 | E-GEOD-65977 | biostudies-arrayexpress

Unique microRNA profiles in EGFR-mutated lung adenocarcinomas

2014-03-10 | GSE48414 | GEO

Analysis of microRNA expression during Epstein-Barr virus encoded LMP1 and LMP2A transfected in TW03 cells

Project description:Epstein-Barr virus has been reported to regulate cellular microRNA expression in B cells. In the present study, we investigated the differential microRNAs modulated by Epstein-Barr virus in Naspharyngeal Carcinoma, using CapitalBio corporation's mammalian miRNA arrays. Three cellular models were used in this study: the human naspharyngeal carcinoma cell line TW03 as a blank control; TW03 transfected with Epstein-Barr virus encoded LMP1; TW03 transfected with Epstein-Barr virus encoded LMP2A

2011-01-13 | E-GEOD-26596 | biostudies-arrayexpress

Global comparison of mouse ES cell lines derived from blastocysts and preblastocysts.

Project description:Standard mouse ES cell derivation protocols use blastocysts at 3.5 dpc, but the efficiency of successful line derivation is low in commonly-used inbred strains, and much lower in other mouse strains. By using 2-cell zona pellucida-free embryos, culturing them on embryonic feeder cells, and passaging the outgrowths in several different media formulations, we have dramatically improved mouse ES cell line derivation efficiency. Mouse ES cell lines derived from blastocyst outgrowths using standard procedures were compared to preblastocyst (2-cell outgrowth)-derived lines, each derived in three different media formulations, using the genome-scale MEEBO gene expression oligo probe set. The overall goal of this microarray study is to determine the overall similarity between cell lines derived using the two methods, in terms of gene expression, as well as to identify important differences. Additionally, we hope to identify effects of the media formulation on gene expression in the cell lines. Seven-condition experiment (two cell types, three derivation conditions, plus one control cell line). 2 biological replicates for each cell line, independently grown and harvested. One dye-swapped pair of arrays per replicate, one probe replicate per array.

2010-08-04 | E-GEOD-17560 | biostudies-arrayexpress

Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer

Project description:Study aims: to identify critical genes involved in non-small cell lung cancer (NSCLC) pathogenesis that may lead to a more complete understanding of this disease and identify novel molecular targets for use in the development of more effective therapies. Methods: Both transcriptional and genomic profiling were performed on 69 resected NSCLC specimens and results correlated with mutational analyses and clinical data to identify genetic alterations associated with groups of interest. Results: Combined analyses identified specific patterns of genetic alteration associated with adenocarcinoma vs. squamous differentiation; KRAS mutation; TP53 mutation, metastatic potential and disease recurrence and survival. Amplification of 3q was associated with mutations in TP53 in adenocarcinoma. A prognostic signature for disease recurrence, reflecting KRAS pathway activation, was validated in an independent test set. Conclusions: These results may provide the first steps in identifying new predictive biomarkers and targets for novel therapies, thus improving outcomes for patients with this deadly disease. Transcriptional profiling of 82 samples of NSCLC using Peter MacCallum in-house 10,500 element cDNA microarray. RNA from 11 pooled cell lines used as reference for each sample. Replicate of 6 samples included.

2010-11-27 | E-GEOD-25326 | biostudies-arrayexpress

Transcriptional profile of Candida parapsilosis CLIB214 versus UPC2 delete, both at 1% oxygen (hypoxia)

Project description:Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis UPC2 delete in hypoxia. RNA was isolated from CLIB214 or upc2 delete grown in YPD medium in hypoxia at 30 degree Celsius for 2 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. 2 dye swaps were perfomed so that 2 out of 4 samples isolated from CLIB214 in hypoxic culture were labeled with Cy3, and 2 were labeled with Cy5

2011-11-30 | E-GEOD-32713 | biostudies-arrayexpress

Transcriptional profile of Candida parapsilosis CLIB214 21% Oxygen (normoxia) versus at 1% oxygen (hypoxia).

Project description:Whole genome microarray were used to generate the transcriptional profile of C. parapsilosis in hypoxic condition. RNA was isolated from CLIB214 grown in YPD medium in normoxia or hypoxia at 30 degree Celsius for 3.5 h, and labeled with Cy3 or Cy5. Four independent biological replicates were compared. Isolates from normoxic condition were labeled with Cy3 and isolates from hypoxic condition were labeled with Cy5.

2011-11-30 | E-GEOD-32712 | biostudies-arrayexpress

Human acute myelogenous leukemia-initiating cells treated with fenretinide

Project description:Transcriptional profiling of human acute myelogenous leukemia (AML) CD34+ cells treated with 5 μM fenretinide. Two timepoints included are 6h, 12h, covering the apoptosis-induction time window of AML CD34+ cells responsing to the fenretinide treatment. We studied gene expression series in human AML CD34+ cells with or without 5 μM fenretinide treatment by cDNA microarray analysis. Several signal transduction pathways are involve, including stress response, NF-kappaB inhibition and p53 inhibition (p<0.05). These findings indicate fenretinide may represent a promising candidate for targeting AML-initiating cells. 6-condition experiment, untreated AML CD34+ cells vs. fenretinide-treated AML CD34+ cells,including 2 time points, for each point the untreated and 5 μM fenretinide treated, independently grown and harvested. Untreated was used to counteracting the background.

2011-11-30 | E-GEOD-33243 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data