Transcriptomic profiling of blood human eosinophils in eosinophilic asthmatic compared to healthy individuals
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Dimitri Pirottin
PROVIDER: E-MTAB-4660 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:We aimed to compare transcriptome in heart and livers of spontaneously hypertensive rat SHR/OlaIpcv (Rat Genome Database ID: 631848) versus coisogenic rat strain SHR-Gja8m1Cub (Rat Genome Database ID: 2293729) using Affymetrix GeneChip® Rat Exon 1.0 ST Arrays in triplicate. Affymetrix GeneChip® Rat Exon 1.0 ST Array was used to determine the transcriptomic characteristics of the SHR and the coisogenic strain SHR-Dca. We extracted total RNA from the kidneys and hearts of 4-month old males of both strains using phenol-chloroform and purified with the RNeasy Mini kit (Qiagen, Valencia, CA, USA) in accordance with the manufacturerâs protocol. The quality of the total RNA was verified by the Agilent 2100 Bioanalyzer system. Double-stranded complementary DNA (cDNA) was synthesized from total RNA. The labeled and fragmented cDNA was pooled for each strain (SHR, SHR-Dca) and tissue (heart, kidney) and hybridized to Affymetrix GeneChip® Rat Exon 1.0 ST Arrays in triplicate (total 12 arrays). The whole hybridization procedure including DNA adjustment was performed according to the protocol recommended by Affymetrix.
2016-07-01 | E-MTAB-4542 | biostudies-arrayexpress
Project description:GeneChip® Mouse Gene 2.0 ST Array for C57BL/6 mouse skin dermal primary lymphatic endothelial cells (Ms LEC) and mouse lymphatic endothelial cell line SVEC4-10 GeneChip® Human Gene 2.0 ST Array for human primary lymphatic endothelial cells (Hu LEC) Total RNA from lymphatic cell line SVEC4-10 were used for GeneChip® Mouse Gene 2.0 ST Array. SVEC4-10 samples, human and mouse LEC samples.
2016-07-20 | E-GEOD-84551 | biostudies-arrayexpress
Project description:Gastric cancer (GC) is one of the most common cancer worldwide. Specific and reliable molecular markers are limited; it is critical to identify new biomarkers for GC to aid in early diagnosis, treatment strategy, and prognosis evaluation. Microarray technology makes it possible to measure the expression levels of thousands of genes, and identifying meaningful and useful molecular targets from these large data. Total RNA was extracted from 10 pairs of GC tissue and adjacent non-tumor mucosa using TRIzol® reagent (Invitrogen, Carlsbad, CA, US) following the manufacturer's instructions. The RNA integrity number (RIN), detected by an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, US), was used to determine the RNA integrity. Total RNA meeting the specified quality criteria (RIN ⥠7.0 and 28S/18S ⥠0.7) were further purified using an RNase-Free DNase Set (Qiagen, Hilden, Germany) and an RNeasy® Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions. Purified total RNA was then used for obtaining biotin-labeled cRNA by applying the GeneChip® 3'IVT Express Kit (Affymetrix, Santa Clara, CA, US), according to the manufacturer's instructions. Then, the GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, Santa Clara, CA, US) was used for performing the array hybridization and wash, with the use of a GeneChip® Hybridization Oven 645 (Affymetrix, Santa Clara, CA, US) and a GeneChip® Fluidics Station 450 (Affymetrix, Santa Clara, CA, US). All arrays were scanned using a GeneChip® Scanner 3000 (Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with the default settings. Raw data were normalized by the MAS 5.0 algorithm in GeneSpring Software 11.0 (Agilent Technologies, Santa Clara, CA, US). The significance analysis of microarray (SAM) was used to identify genes that were differentially expressed between the GC and normal tissues. Genes were considered to be differentially expressed when the Tumor versus Normal signal log ratio values were â¥2 or â¤0.5.
2016-04-07 | E-GEOD-79973 | biostudies-arrayexpress
Project description:Differential expression of regulatory genes of reference strain P. aeruginosa PA01, involved in the quorum sensing was analyzed using Microarray. Total RNA was isolated from reference strain P. aeruginosa PA01, grown with or without bacterial extracts (0.1 mg/ml) using TRI reagent. Total RNA was quantified, and 10 µg RNA was converted to cDNA, fragmented and labelled by following GeneChip® P. aeruginosa PA01 genome array user manual . Labelled cDNAs were hybridized with P. aeruginosa genome array gene chip , washed and stained. Hybridized chips were scanned, processed and analyzed using expression console and transcriptome analysis console.
2017-04-12 | E-MTAB-5693 | biostudies-arrayexpress
Project description:gd T cells have an important yet incompletely defined role in inflammation associated with a variety of infectious and autoimmune conditions. To better understand the precise roles of gd T cells relative to ab T cells in a specific infection, we utilized Salmonella Enterica Serovar Typhimurium (S. typhimurium) infection in cattle as it is a leading cause of disease in cattle and closely approximates S. typhimurium-induced enterocolitis in humans. To best represent phenotype and gene expression changes occurring in the gut mucosa early in S. typhimurium infection, gd and ab T cells were collected directly from the mesenteric lymphatic ducts and analyzed by FACS or immediately sorted and processed for microarray analysis. Gene expression profiles were compared at intervals during infection within T cell subsets. The majority of gene expression changes in both subsets occurred 48 hours after infection. In response to S. typhimurium infection there was an increase in expression of several genes in gd T cells which were indicative of activation, proliferation and innate function, whereas in ab T cells gene expression changes suggested a lack of S. typhimurium-specific response. This work represents the first focus on gene expression trends in tissue-derived T lymphocytes in an in vivo model that is highly relevant to human S. typhimurium-induced enterocolitis. Experiment Overall Design: For one mock infection (calf 156) and two experimental S. typhimurium infections (calves 112 and 162), gd and ab lymphatic T cells were stained with GD3.8 directly conjugated to FITC, washed, and sorted on a Vantage SE cell sorter (BD Immunocytometry Systems) as previously described. Sorted gd and ab T cells were collected directly into TRIzol reagent (Invitrogen; calf 112) and lysed or suspended in Buffer RLT (Qiagen; calves 156 and 162) and lysed using Qiashredder columns, then frozen at -80oC. RNA was extracted following the manufacturerâs protocol for Trizol (Invitrogen) extraction, or RNeasy (Qiagen) column purification, assessed on a Bioanalyzer 2100 (Agilent Technologies), and amplified either using Affymetrix Two-cycle (calf 112) target labeling protocol with 100 ng total RNA or the One-cycle protocol (calves 156 and 162) with approximately 1.6 micrograms of total RNA as described in the GeneChip® Expression Analysis Technical Manual (June 2004). Hybridizations to Genechip® Bovine Genome Arrays (Affymetrix) were performed with 15 micrograms biotin labeled cRNA. Washing and staining was performed in the GeneChip® Fluidics Station 450 using the Midi_euk2v3 protocol. Chip scans were performed on the Affymetrix GeneChip® Scanner 3000. GeneChip® Operating Software (GCOS v.1.1, Affymetrix) was used for data collection. Experiment Overall Design: Table I represents annotated genes of potential interest that changed 2 fold or greater in expression between 0 and 48 hours post-Salmonella infection (calves 112 and 162) or mock-infection (calf 156) in T cell subsets.
2008-11-08 | E-GEOD-3439 | biostudies-arrayexpress
Project description:The cause of mental retardation in one-third to one-half of all affected individuals is unknown. Microscopically-detectable chromosomal abnormalities are the most frequent recognized cause, but gain or loss of chromosomal segments that are too small to be seen by conventional cytogenetic analysis has been found to be another important cause. Array-based methods offer a practical means of performing a high-resolution survey of the entire genome for submicroscopic copy number variants. We studied 100 children with idiopathic mental retardation and their parents using the Affymetrix GeneChip® Mapping 100K Assay and found de novo duplications as small as 1.1 Mb in three cases, de novo deletions as small as 178 kb in eight cases, and unsuspected mosaic trisomy 9 in another case. This technology can detect at least twice as many potentially pathogenic de novo copy number variants as conventional cytogenetic analysis in people with mental retardation. Experiment Overall Design: Using the Affymetrix GeneChip® Mapping 100K Assay we studied 100 trios that each included one child with idiopathic mental retardation (MR) and both of his/her unaffected biological parents. We also tested 10 unaffected siblings of the MR children from 10 of the above families. In addition, we analyzed 7 trios (child and both unaffected biological parents) as positive controls with previously identified chromosomal aberrations. Experiment Overall Design: Within each sample ID the four digit number refers to a family. Following this four digit family number, 'c' indicates child with MR, 'm' means unaffected mother, 'f' means unaffected father and 's' means unaffected sibling.
2008-06-21 | E-GEOD-7226 | biostudies-arrayexpress
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