Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from LCL samples from patients with global developmental delay and autistic features and normal controls

ABSTRACT: We analyzed the whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) from patients (n=2), carriers (n=2), and unrelated normal controls (n=3), all performed in duplicates using Affymetrix GeneChip Human Exon 1.0 ST arrays, to identify genes and pathways that are significantly dysregulated in affected individuals. Moreover, we have performed global transcriptional profiling in whole blood from patients (n=2) and healthy controls (n=13) using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Global transcriptional profiling of affected individuals and controls revealed significant alterations of genes and pathways in a pattern consistent with previous microarray studies of autism spectrum disorder patients. Genome-wide gene-level expression changes for samples from cultured lymphoblastoid cell lines from patients with global developmental delay and autistic features (n=2), carriers (n=2), and unrelated healthy controls (n=3), all performed in duplicate, using Affymetrix GeneChip® Human Exon 1.0 ST arrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Dilek Colak

PROVIDER: E-GEOD-29918 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from patients with global developmental delay and autistic features and normal controls

Project description:We analyzed the whole-genome mRNA expression profiling of cultured lymphoblastoid cell lines (LCLs) from patients (n=2), carriers (n=2), and unrelated normal controls (n=3), all performed in duplicates using Affymetrix GeneChip Human Exon 1.0 ST arrays, to identify genes and pathways that are significantly dysregulated in affected individuals. Moreover, we have performed global transcriptional profiling in whole blood from patients (n=2) and healthy controls (n=13) using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. Global transcriptional profiling of affected individuals and controls revealed significant alterations of genes and pathways in a pattern consistent with previous microarray studies of autism spectrum disorder patients. Whole-genome mRNA expression profiles of samples from whole blood from patients with global developmental delay and autistic features (n=2) and healthy controls (n=13) using Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays.

2014-08-01 | E-GEOD-29691 | biostudies-arrayexpress

Expression data from patients with global developmental delay and autistic features and normal controls

2014-08-01 | GSE29691 | GEO

Expression data from LCL samples from patients with global developmental delay and autistic features and normal controls

2014-08-01 | GSE29918 | GEO

Role of GM-NM-1(olf) in Familial and Sporadic Adult-Onset Primary Dystonia

Project description:Gene expression studies were performed to identify pathways possibly dysregulated by mutant in the gene GM-NM-1(olf). These experiments employed RNA derived from lymphoblastoid cell lines established for 4 affected carriers and 4 non-carriers. In comparison to endogenous control and other dystonia-associated genes, GNAL was expressed at relatively low levels in lymphoblastoid cell lines. Comparison of whole blood expression profiles of mutation carrying dystonia patients with normal controls

2013-01-26 | E-GEOD-43771 | biostudies-arrayexpress

MudPIT proteomic profiling of lymphoblastoid cells from Nasu-Hakola subjects

Project description:Proteomic analysis was performed, by means of MudPIT platform, on Lymphoblastoid cell lines (LCLs) immortalized from B-Lymphocytes. LCLs were collected from each subject of an italian family, native of a restricted area of northern Italy and consisted of seven components: two patients with homozygous C-to-T mutation at position 97 in exon 2 of TREM2 gene (Ho); four healthy carriers with heterozygous mutation (He), and one healthy individual (Wt).

2021-06-15 | MSV000087622 | MassIVE

Exon-expression profiling of CD4+ T cells derived from HTLV-1-infected individuals with or without malignancy

Project description:T-cell clones were obtained by limiting dilution culture of PBMC of HTLV-1 carriers. Exon expression profiling was performed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. Gene version of CEL files 01 to 12 are presented in GSE46518. The main objectives were to assess whether transcriptional and post-transcriptional modifications associate with HTLV-1 infection in vivo. To this end, T-cell clones, infected or not by HTLV-1, were obtained by limiting dilution culture of PBMC derived from HTLV-1 carriers. Tumor cells derived from patients with an acute form ATLL. Exon expression profiles of cloned T-cells and ATLL cells was analyzed using Affymetrix exon array (Affymetrix Human Exon 1.0 ST Array) according to the manufacturer's instructions. Given that T-cell activation is known to modify alternative exon usage, microarray analysis was carried-out with unstimulated and PHA-stimulated CD4+ T cell clones.

2015-11-01 | E-GEOD-52244 | biostudies-arrayexpress

Global gene expression analysis of human iPSC-derived Retinal Pigmented Epithelial (RPE) cells from LCA patients and unaffected persons

Project description:Our purpose was to investigate genes and molecular mechanisms involved in patients with Leber congenital amaurosis (LCA). Fibroblasts from two unrelated clinically-identified patients (Coriell) were reprogrammed to pluripotency by retroviral transduction. These human induced Pluripotent Stem Cells (hiPSCs) were differentiated into neural stem cells (NSC) that mimicked the neural tube stage and retinal pigmented epithelial (RPE) cells that could be targeted by the disease. A genome wide transcriptome analysis was performed with Affymetrix Exon Array GeneChip®, comparing LCA-hiPSCs derivatives to controls. The aim was to identify differentially expressed genes which may be associated with early developmental defect before the establishment of mature retinal circuitry.

2015-01-21 | GSE43926 | GEO

Global gene expression analysis of human iPSC-derived Neural Stem Cells (NSC) from LCA patients and unaffected persons

2015-01-21 | GSE43924 | GEO

Genome-wide consequences of compromised NMD and their relavence for variable clinical phenotype of patients with UPF3B mutations [CNV]

Project description:Nonsense-mediated mRNA decay (NMD) surveillance pathways are best known to be involved in the degradation of mRNA with premature termination codons (PTCs). More recent studies demonstrate that the role of NMD pathways goes well beyond the degradation of PTC containing mRNA, into the regulation of cell function and thus normal development. We have taken advantage of the availability of naturally occurring loss of function mutations in the UPF3B gene, a major component of the exon junction complex (EJC), to inquire about genome-wide consequences of compromised NMD. We identify that about 5% of the lymphoblastoid cell transcriptome is directly or indirectly impacted upon in patients with UPF3B mutations with minimal effect on alternative splicing. We identify UPF3A-NMD as a likely, major modifier of the UPF3B patient phenotype through variable UPF3A protein stabilisation. Among the most consistently deregulated direct targets of UPF3B-NMD we identify the ARHGAP24 as the most likely gene implicated in the neuronal phenotype of UPF3B patients. To assess the impact of UPF3B-NMD deficiency on human transcriptome, we sequenced polyA RNA extracted from lymphoblastoid cell lines of patients (n=4) and controls (n=2). We complemented the analysis using Affymetrix Human Exon 1.0 St array using total RNA of the same cell line from patients (n=5, 3 of whom were also sequenced) and controls (n=5). Moreover, we overlapped identified differently expressed genes with copy number variation data of the patients, obtained using Illumina Human Omniexpress chip, to exclude possible false positive.

2011-11-01 | E-GEOD-27412 | biostudies-arrayexpress

Transcriptional and post-transcriptional analysis of CD4+ T cell clones deriving from HTLV-1 infected individuals

2014-12-03 | E-GEOD-46518 | biostudies-arrayexpress