Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ShRNA cassette sequencing from disomic and trisomic fibroblasts cultured in the presence of shRNA kinome library for 14 days

ABSTRACT: Kinome-wide shRNA screen to identify kinases differentially required for survival of cells disomic and trisomic for chromosome 21 Cells were transduced in triplicate and propagated for 14 days to allow for enrichement or depletion of shRNAs from the population

ORGANISM(S): Homo sapiens

SUBMITTER: Ahwan Pandey

PROVIDER: E-GEOD-79840 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Trisomy 21 consistently activates the interferon response.

Sullivan Kelly D KD Lewis Hannah C HC Hill Amanda A AA Pandey Ahwan A Jackson Leisa P LP Cabral Joseph M JM Smith Keith P KP Liggett L Alexander LA Gomez Eliana B EB Galbraith Matthew D MD DeGregori James J Espinosa Joaquín M JM

eLife 20160729

Although it is clear that trisomy 21 causes Down syndrome, the molecular events acting downstream of the trisomy remain ill defined. Using complementary genomics analyses, we identified the interferon pathway as the major signaling cascade consistently activated by trisomy 21 in human cells. Transcriptome analysis revealed that trisomy 21 activates the interferon transcriptional response in fibroblast and lymphoblastoid cell lines, as well as circulating monocytes and T cells. Trisomy 21 cells s ...[more]

PMID: 27472900

Similar Datasets

shRNA cassette sequencing from disomic and trisomic fibroblasts cultured in the presence of shRNA kinome library for 14 days

Project description:Kinome-wide shRNA screen to identify kinases differentially required for survival of cells disomic and trisomic for chromosome 21

2016-07-29 | GSE79840 | GEO

RNAseq from disomic and trisomic fibroblasts and lymphoblastoids

Project description:RNA was sequenced from individuals Disomic and Trisomic for chromosome 21 to identify consistent changes in gene expression across individuals

2016-07-29 | GSE79842 | GEO

RNAseq from disomic and trisomic T cells and monocytes

Project description:RNA was sequenced from Disomic and Trisomic individuals for chromosome 21 to identify consistent changes in gene expression across individuals

2016-07-29 | GSE84531 | GEO

RNAseq from disomic and trisomic fibroblasts and lymphoblastoids

Project description:RNA was sequenced from individuals Disomic and Trisomic for chromosome 21 to identify consistent changes in gene expression across individuals Cells were cultured at subconfluency and RNA harvested for sequencing

2016-07-29 | E-GEOD-79842 | biostudies-arrayexpress

RNAseq from disomic and trisomic T cells and monocytes

Project description:RNA was sequenced from Disomic and Trisomic individuals for chromosome 21 to identify consistent changes in gene expression across individuals Cells were cultured at subconfluency and RNA harvested for sequencing

2016-07-29 | E-GEOD-84531 | biostudies-arrayexpress

Transcriptome analysis of genetically matched human induced pluripotent stem cells disomic or trisomic for chromosome 21

Project description:Trisomy of chromosome 21, the genetic cause of Down syndrome, has the potential to alter expression of genes on chromosome 21, as well as other locations throughout the genome. These transcriptome changes are likely to underlie the Down syndrome clinical phenotypes. We have employed RNA-seq to undertake an in-depth analysis of transcriptome changes resulting from trisomy of chromosome 21, using induced pluripotent stem cells (iPSCs) derived from a single individual with Down syndrome. These cells were originally derived by Li et al, who genetically targeted chromosome 21 in trisomic iPSCs, allowing selection of disomic sibling iPSC clones. Analyses were conducted on trisomic/disomic cell pairs maintained as iPSCs or differentiated into cortical neuronal cultures.

2018-04-09 | GSE101942 | GEO

Kinome analysis of CD151 overexpressing Jurkat T cells

Project description:The effect of CD151 expression onto the kinome of Jurkat T cells was assessed using kinome analysis. CD151 was expressed in Jurkat T cells by retroviral transduction based on a pMSCV vector. Entrez Gene: 977 UniProtKB: P48509 Jurkat T cells were transduced with the MSCV-CD151 vector and successfully transduced cells were selected using puromycin. For the kinome array experiments 3 independent samples of Jurkat cells and three independent samples of J-CD151 cells were collected. To minimize unspecific background signals, lysates from Jurkat and J-CD151 T cells harvested at different growth stages, which were then pooled to provide one sample prior to loading on the Kinexus antibody microarrays.

2017-09-30 | E-MTAB-5978 | biostudies-arrayexpress

Kinome analysis of human CD151+ and CD151- T cells in the absence or presence of IL-2 stimulation

Project description:Primary human T cells from healthy donors were sorted using a FACSAria II to obtain CD3+CD4+CD151+ and CD3+CD4+CD151- populations. To perform kinome analysis using Kinex™ microarrays, 50 µg of lysate protein from each sample were labeled with a proprietary fluorescent dye according to the manufacturers instructions (Kinexus, Canada). The utilized KAM-850 chips were spotted in duplicates with over 850 antibodies: 510 pan-specific antibodies used in the chip allows for the detection of 189 protein kinases, 31 protein phosphatases and 142 regulatory subunits of these enzymes and other cell signaling proteins. 340 phospho-specific antibodies tracked the unique phosphorylation of 128 sites in protein kinases, 4 sites in protein phosphatases and 155 sites in other cell signaling proteins. The background-corrected raw intensity data were logarithmically transformed with base 2. Z scores were calculated by subtracting the overall average intensity of all spots within a sample from the raw intensity for each spot, and Z score ratios were calculated by dividing Z scores by the standard deviations (SD) of all of the measured intensities within each sample. To minimize unspecific background signals, lysates from cells from 5 different donors were sorted and the corresponding populations were pooled to provide one sample prior to loading on the Kinexus antibody microarrays. 16JN20-KAM880 Kit-K012003211-19123.txt contains the original data for the CD4+CD151- T cell population at baseline. 16JN20-KAM880 Kit-K012003211-19124.txt contains the original data for the CD4+CD151- T cell population following stimulation with 30 U/ml IL-2 for 24 hours. 16JN21-KAM880 Kit-K012003229-19125.txt contains the original data for the CD4+CD151+ T cell population at baseline. 16JN21-KAM880 Kit-K012003229-19126.txt ontains the original data for the CD4+CD151+ T cell population following stimulation with 30 U/ml IL-2 for 24 hours.

2017-09-30 | E-MTAB-5977 | biostudies-arrayexpress

Blood cells with trisomy 21 overreact to heat shock stress [PRO-seq]

Project description:Lymphoblastoid cells trisomic for chromosome 21 activate the heat shock response more robustly than disomic cells.

2023-04-21 | GSE173537 | GEO