Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The effect of C/EBPepsilon in differentiated granulocytes: cDNA microarray of C/EBPepsilon knock out mice vs C57BL/6 mice bone marrow cells

ABSTRACT: To identify target genes of C/EBPepsilon in differentiated granulocytes, total RNA were purified from sorted Gr-1intermediate/Mac-1+ and Gr-1hi/Mac-1+ cells of C/EBPepsilon knock out and C57BL/6 wild type mice using RNeasy Mini Kit (Qiagen). The differences of their expression pattern were compared with Illumina Mouse WG-6v2 Expression Chip platform. Raw Illumina BeadArray data in IDAT format were preprocessed using the open-source Bioconductor package illuminaio with the Illumina array design formation BGX file downloaded from NCBI, GEO accession: GPL6887. Following the preprocessing, the expression data were normalized by applying control background correction, log transformation and inter-quantile normalization using the neqc function from the limma bioconductor package. This allowed us to compare the transcriptomic consequences of C/EBPepsilon in two independent populations.

ORGANISM(S): Mus musculus

PROVIDER: GSE73835 | GEO | 2017/06/02

SECONDARY ACCESSION(S): PRJNA298235

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Medulloblastoma Methylation Profiling

Project description:Genome wide DNA methylation profiling of human medulloblastoma. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Preprocessed data performed using Illumina normalization in the minfi package as described in Sturm et al, Cancer Cell, 2012.

2015-11-19 | GSE75153 | GEO

TFH cell dynamics in Rhesus Monkeys during SIV infection

Project description:Cells from SIV-negative (SIVnegative_p17, n=5; SIVnegative_p18, n=5) and SIV-chronic (ChronicSIVinfection_p18, n=6) SP tissues were sorted for microarray studies. RNA samples were prepared using the Illumina beads station assay and hybridized to the Illumina HumanHT-12 version 4 Expression BeadChip according to the Illumina’s instruction. The data were normalized with the quantile normalization method of Bioconductor package limma . Missing values were imputed with R package impute (http://cran.rproject.org/web/packages/impute/index.html). Genes with significant differential expression levels were identified using Bioconductor limma package with >= 1.5 fold change (up or down), the false discovery rate (FDR) adjusted P value < 0.05.

2012-06-19 | GSE38795 | GEO

Epigenetic methylation chip analysis of childhood ependymoma PFA subgroup patient samples [Infinium 450K Methylation Beadchip]

Project description:DNA methylation analysis was perfomed using Infinium 450K Methylation BeadChip platform on 140 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

2023-06-01 | GSE226960 | GEO

Epigenetic methylation chip analysis of childhood PFA ependymoma patient samples [EPIC Methylation]

Project description:DNA methylation analysis was perfomed using Infinium EPIC Methylation BeadChip platform on 65 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

2023-06-01 | GSE226895 | GEO

Transcription profiling of Mac-1+, c-Kit+ myeloid progenitor cells from mice homozygous for the p42-specific knock-out Cebpa mutation and independently transplanted with leukemic bone marrow, and from control mice heterozygous for Cebpa mutation

Project description:5000 Mac-1+, c-Kit+ myeloid progenitor cells from 3 mice homozygous for the p42-specific knockout Cebpa mutation and independently transplanted with leukemic bone marrow, or from 3 control mice heterozygous for Cebpa mutation, were isolated by FACS. Total RNA was extracted and fluorescence labeled for hybridization to MOE430.2 gene expression arrays. cRNA synthesis entailed 2 rounds of linear amplification using the T7 cRNA protocol provided by the manufacturer. Hybridization and washing was performed according to Affymetrix GeneChip expression analysis technical protocols. Microarray data were analyzed in the R statistical computing framework using the Bioconductor suite. Hybridization quality was assessed with the Bioconductor package arrayQualityMetrics and the raw fluorescence data were processed using the GCRMA method.

2008-04-08 | E-MEXP-1444 | biostudies-arrayexpress

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

Expression of cyclophilin B is associated with malignant progression and regulation of genes

Project description:Microarray was conducted on Illumina Human Ref-6 Version 2 Expression Chip (Illumina, San Diego, CA). Three independent cultures were used for RNA isolation with RNeasy plus mini kit (Qiagen, Valencia, CA). RNA quality was checked by Agilent Bioanalyzer (Agilent, Santa Clara, CA). An Ambion labeling kit was used for labeling cDNA followed by hybridization to Illumina chips. ChIP scan data was extracted by Illumina Beadstudio and subsequently analyzed using Bioconductor lumi package.

2009-04-03 | GSE15505 | GEO

Genome-wide CpG expression analysis of human white blood cells in obese patients under a weight loss treatment.

Project description:Genome wide expression profiling of white blood cells in obese patients under two different diets (The American Heart Association's Diet and RESMENA diet (Zulet MA et al., Nutr Hosp. 2011 Jan-Feb;26(1):16-26. )) in order to reduce weight. The Illumina HumanHT-12 v4 Expression BeadChip Kit was used, which assayed 47,000 probes.A total of 24 RNA was purified from white blood cells using a TRIZOL RNA Isolation Protocol (Life technologies) and 500 ng of starting material were used as input for the Illumina TotalPrep Amplification Kit. Next, The Illumina GenomeStudio Gene Expression Software Module (v 1.9.0, Illumina, USA) was used to extract the signal intensities of each gene expression probe, which were then further preprocessed using the lumi package of Bioconductor in R. The preprocessing included background correction of the gene expression data, followed by log2-transformation and quantile normalization. It also automatically removes the control probes, leaving only the regular probes. We keep probes that are expressed in at least one individual according to a detection p-values of 5%. Assays containg SNPs within the probe were removed.

2019-10-30 | E-MTAB-2604 | biostudies-arrayexpress

Medulloblastoma Methylation Profiling

2015-11-19 | E-GEOD-75153 | biostudies-arrayexpress

TFH cell dynamics in Rhesus Monkeys during SIV infection

2012-06-18 | E-GEOD-38795 | biostudies-arrayexpress