ArrayExpress Archive - Experiments (first 25 of 30137)

E-MTAB-688 - Transcription profiling by array of human MCF7 breast cancer cells with FOXP3 target gene expression with and without MOF knockdown

Sat, 26 May 2012 00:00:00 +0000

As we clarified before, FOXP3 gene is an X-linked tumor suppressor for both human and mouse. And we also clarified direct target genes of FOXP3 in human cancer cells. Recently we identified that MOF, a histone acetyltransferase, can be a FOXP3's molecular partner to regulate target gene expression. We conducted a microarray analysis using MCF7 cell, a human breast cancer cell line, with FOXP3-tet-off system with and without MOF knock down before and after FOXP3 overexpression. After 48 hrs of RNAi treatments in MCF7 cells, FOXP3 was overexpressed and those cells were cultured for additional 48 hrs. Total RNA were extracted using Qiagen's RNeasy column and were applied to Affymetrix Human U133 Plus 2.0 array according to the manufacture's protocol.

E-MTAB-1015 - Genome-wide Analysis of Sp2 Occupancy and Expression Profiling Establish Sp2 as a Sequence-specific Transcription Factor Regulating Fundamental Cellular Processes - Expression Profiling

Thu, 24 May 2012 00:00:00 +0000

Mouse embyronic fibroblasts (MEFs) were depleted for transcription factor Specificity Factor 2 (Sp2) via Cre-Recombinase, harvested either 7 days or several weeks post infection and their expression profile compared to mock-infected MEFs.

E-MTAB-994 - ChIP-seq of Sp2 in wild type and deltaSp2 mouse embryonic fibroblasts and human embryonic kidney cell line HEK293

Thu, 24 May 2012 00:00:00 +0000

Genome-wide Analysis of Sp2 Occupancy and Expression Profiling Establish Sp2 as a Sequence-specific Transcription Factor Regulating Fundamental Cellular Processes - ChIPseq

E-MTAB-1143 - The Pdx1 Cistrome of Pancreatic Islets

Wed, 23 May 2012 00:00:00 +0000

We performed global location analysis of Pdx1 occupancy in mouse and human islets.

E-MTAB-1136 - MicroRNA profiling by array of human osteosarcoma and their normal bone counterpart

Mon, 21 May 2012 00:00:00 +0000

Profiling array: in order to investigate the microRNAs differentially expressed between osteosarcoma and their normal bone counterpart. Specimens were kept at 4 C in RNAlater for up to 1 week, then stored at 80 C. When formal pathologic interpretation of histology from other portions of the biopsy specimen rendered a diagnosis of osteosarcoma, the RNA-preserving tissue specimens were banked and annotated. In preparation for these specific experiments, total RNA was extracted from banked specimens with the TRIzol reagent and method (Invitrogen). Control samples were derived from to-be-discarded bone fragments obtained from similarly consented patients undergoing debridement surgeries for acute, traumatic injuries to the long bones.

E-MEXP-3636 - Exploring copy number variation in the rabbit genome by array comparative genome hybridization

Mon, 21 May 2012 00:00:00 +0000

First investigation of Copy Number Variations in the the Oryctolagus cuniculus (Rabbit) genome by array comparative genome hybridization (aCGH)

E-MEXP-3304 - CovRS response in S. agalactiae NEM316 strain

Mon, 21 May 2012 00:00:00 +0000

Analysis of the CovRS response in S. agalactiae NEM316 strain with microarrays

E-MEXP-3237 - Transcription profiling by array of Streptococcus agalactiae NEM316 wild type and rogB mutant strains

Mon, 21 May 2012 00:00:00 +0000

transcritpomic analysis of rogB mutant in NEM316 S. agalactiae strain

E-MEXP-3236 - rga response

Mon, 21 May 2012 00:00:00 +0000

comparison of the transcriptionnal response of the rga mutant and the wild type in S. agalactiae NEM316 strain

E-TABM-1158 - RIp-chip experiments with proteins that do not contain RNA-binding domains

Sun, 20 May 2012 00:00:00 +0000

In order to assess the prevalence of cotranslational assembly of protein complexes we performed RIp-chip experiments with many proteins that do not conatin RNA-binding motifs

E-MEXP-3567 - Transcriptional profiling by array of blood samples from Malawian children to find novel biomarker combination for improving the diagnosis of serious bacterial infections

Sun, 20 May 2012 00:00:00 +0000

We aimed to discover a combination of reliable and functionally important biomarkers of severe bacterial infection (SBI) using transcriptomics, and to evaluate their clinical validity.

E-MEXP-3499 - ChIP-chip by array of human HeLa cells exposed to 1% oxygen (hypoxia) or 21% oxygen (normoxic control) to study the DNA binding profile of endogenous HIF1A on proximal promoters.

Sun, 20 May 2012 00:00:00 +0000

DNA binding profiling of endogenous HIF1A on proximal promoters in human HeLa cells exposed to 1% oxygen (hypoxia), using normoxic cells (21% oxygen) as reference.

Biological background: The Hypoxia Inducible Factor Family of transcription factors is proposed as the main orchestrator of the cellular response to hypoxia. HIFs are heterodimers of a HIF alpha and a HIF beta subunit. HIF alpha protein stability is regulated by oxygen-dependent proteasomal degradation, and hence HIFs are strongly stabilized in hypoxia.

Purpose of the study: a number of HIF1 ChIP-chip studies have been reported, employing various cell types, array platforms and HIF antibodies, and the overlap of HIF binding locations in these studies is relatively small. The aim of this study was to characterize HIF1 binding in an additional cell line (HeLa), and employing a different HIFalpha antibody.

Experimental design: We conducted a total of six hybridizations employing four biological replicates. For two biological replicates, we performed dye-swap technical replicate experiments.

Results summary: We identified 55 HIF binding locations in HeLa cells (FDR<2%). While this number is relatively low compared to previous studies, presumably due to limiting antibody sensitivity, the overlap with data from other cell lines is comparable to our HeLa data.

E-MEXP-3635 - Transcriptomic Assay of CD8 2012-05-15

Thu, 17 May 2012 00:00:00 +0000

In this study, Genome-wide transcriptomes of CD8+ T cells from HCV/HIV co-infected or mono-infected treatment-naïve individuals were analyzed by using microarray assays. Pairwise comparisons were performed and differentially expressed genes were identified followed by quantitative real time PCR (qRT-PCR) validation. To identify the important functional categories, Directed Acyclic Graphs (DAG) from Web-based Gene SeT AnaLysis Toolkit (WebGestalt) was used to find out Gene Ontology (GO) categories with significantly enriched gene numbers. The enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were also obtained by using the similar methods in the same website.

E-MEXP-49 - Transcription profiling of wild type fly heads (CantonS) and eye-less fly heads (sine occulis)

Thu, 17 May 2012 00:00:00 +0000

To identify the eye-enriched genes by comparing the mRNA expression profiles from wild type fly heads (CantonS) and eye-less fly heads (sine occulis).

E-MEXP-3215 - WT vs. TPP potato

Wed, 16 May 2012 00:00:00 +0000

Comparison between wildtype potato tubers and three transgenic lines with reduced T6P content

E-TABM-1216 - Transcriptional profiling by array of neural embryonic stem cells (ESTn) to test their dose responses to six compounds.