Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression profiling of small bowel adenocarcinoma

ABSTRACT: The whole genome DASL HT assay was used in combination with the HumanHT-12 v4 BeadChip for screening normal and tumour tissue in a retrospective 28 sample cohort of small bowel adenocarcinoma patients. Non-normalized and average normalized (background subtracted) data

ORGANISM(S): Homo sapiens

PROVIDER: GSE61465 | GEO | 2015/09/03

SECONDARY ACCESSION(S): PRJNA261242

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Gene expression profiling of small bowel adenocarcinoma

Project description:The whole genome DASL HT assay was used in combination with the HumanHT-12 v4 BeadChip for screening normal and tumour tissue in a retrospective 28 sample cohort of small bowel adenocarcinoma patients. Non-normalized and average normalized (background subtracted) data Comparing differences in gene expression in a matched normal tumour cohort of 28 small bowel adenocarcinoma patients.

2015-09-03 | E-GEOD-61465 | biostudies-arrayexpress

Integrated molecular portrait of triple negative breast tumors from Mexican women using archived clinical samples

Project description:Triple negative breast tumours from archived formalin fixed paraffin embeded samples of the National Cancer Institute of Mexico were analyzed for differential gene expressión. Transcriptomic analysis of the 12 tumor samples was done with the FFPE-designed WG-DASL HT assay (Illumina) according to manufacturer’s instructions. This assay measures 29,285 annotated transcripts derived from the RefSeq database corresponding to 20,727 unique genes. Briefly, 200ng of total RNA were reverse-transcribed into biotinylated cDNA, which was then primer-extended with the Assay Specific Oligos. The cDNA was then amplified with universal primers and hybridized to Illumina Human WG DASL HT Expression BeadChip arrays. The Illumina Genome Studio V2010.2 was used to obtain the signal values (AVG-Signal), with no normalization and no background subtraction.The performance of hybridizations was evaluated by assessing the presence of outliers and the noise-to-signal ratios by calculating the ratio of centiles P95/P05 prior to normalisation for each sample. We defined outliers as samples with P95/P05 ratio <9.5. All samples were found to show a correct noise-to-signal ratio (P95/P05>9.6). For differential gene expression analysis, the public dataset GSE32124, which includes 33 fresh frozen tissue samples, generated on the Illumina HumanHT-12 v4.0 beadChip, and which contains 99.98% of the 29,285 probes of the Human WG DASL HT BeadChip was used as normal breast tissue control.

2015-05-12 | E-GEOD-62502 | biostudies-arrayexpress

Effect of LIMD1 knockdown on gene expression in Human Bronchial Epithelial Cells (HBECs)

Project description:HBECs were untreated, treated with scrambled siRNA (80nM) or LIMD1 targeting siRNA (80nM) for 72 hours. Total RNA was extracted and gene expression was measured using Illumina HumanHT-12 v4 Expression BeadChip array.

2018-05-22 | GSE114692 | GEO

DNA methylation screening of small bowel adenocarcinoma

Project description:Illumina Infinium 450k screening of normal and tumour tissue in a retrospective 28 sample cohort of small bowel adenocarcinoma patients. Average signal and beta values normalised to internal Illumina controls. Comparing DNA methylation differences in a matched normal tumour cohort of 28 small bowel adenocarcinoma patients.

2015-09-03 | E-GEOD-61467 | biostudies-arrayexpress

MicroRNA-7-5p mediates the anti-oncogenic effect of hepatocyte growth factor in the MCF-10A mammary epithelial cell

Project description:Genome wide expression profiling of breast normal cell line MCF-10A. The Illumina HumanHT-12 v4 Expression BeadChip was used to obtain expression profiles. This profiling indicates that MicroRNA-7 mediates the activity of HGF to suppress oncogenic proteins, which inhibits cancer progress.

2017-12-06 | GSE102758 | GEO

DNA methylation screening of small bowel adenocarcinoma

2015-09-03 | GSE61467 | GEO

shRNA kinome screen identifies TBK1 as therapeutic target for HER2+ breast cancer

Project description:Microarray analysis was performed at the UHN Microarray Centre (UHNMAC, Ontario, Canada) using Illumina HumanHT-12 v4 BeadChip with 500 ng of total RNA prepared by RNeasy mini kit (QIAGEN, Cat. No. 74104). Samples from HCC1954 cells with 3-day treatment of TBK1-II at 4 uM were used to compare with vehicle-treated controls. Microarray data was processed and normalized by lumi package from BioConductor in R with Quantile Method. Difference between the samples were calculated by Bayesian statistic using limma package from BioConductor in R to obtain Moderated T value for subsequent Pathway analysis.

2013-12-26 | GSE53658 | GEO

Inflammatory Bowel Disease StOlav

Project description:Expression profiling of human colon mucosa samples aquired from inflammatory bowel disease patients and healthy controls. Expression profiling was done using Illumina Human HT-12 arrays, and data analysis was performed using tools from the Bioconductor package

2012-09-12 | E-MTAB-184 | biostudies-arrayexpress

Illumina Bead expression array data from Human IgE+ and IgG+ B cell subsets

Project description:Human in-vitro differentiated IgE+ and IgG+ Germinal Centre B cells, plasma blasts and plasma cells were isolated by flow cytometry and subjected to transcriptome analysis using the Illumina HumanHT-12 v4 Expression BeadChip array platform. B cells derived from 4 donors are submitted for each cell population.

2017-09-01 | GSE99948 | GEO

Illumina Bead expression array data from Human B cells treated with miR-29 over expression

Project description:Human Tonsillar B cells were isolated and transfected with miR-29 mimic molecules or transfection controls. B cells were subsequently cultured in class switching media for 24 hours and subjected to transcriptome analysis using the Illumina HumanHT-12 v4 Expression BeadChip array platform. B cells derived from 3 donors are submitted.

2020-06-24 | GSE100735 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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