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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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SelT knockdown mouse fibroblast cells vs control cells

ABSTRACT: Analysis of gene expression in NIH 3T3 cells stably knockdown for Selt (GenBank accession number NM_001040396) using vector based siRNA technique in comparison to gene expression of vector transfected NIH 3T3 cells. siSelT-1 construct (spanning nucleotides 205-224 of Selt, GenBank accession number NM_001040396) vs vector control; siSelT-5 construct (spanning nucleotides 971-989 of Selt, GenBank accession number NM_001040396) vs vector control; Two replicates per array for each oligos were carried out at different time points using RNA from different cultures of knockdown cells.

ORGANISM(S): Mus musculus

SUBMITTER: Aniruddha Sengupta

PROVIDER: E-GEOD-17087 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Selenoprotein T deficiency alters cell adhesion and elevates selenoprotein W expression in murine fibroblast cells.

Sengupta Aniruddha A Carlson Bradley A BA Labunskyy Vyacheslav M VM Gladyshev Vadim N VN Hatfield Dolph L DL

Biochemistry and cell biology = Biochimie et biologie cellulaire 20091201 6

Mammalian selenoproteins have diverse functions, cellular locations, and evolutionary histories, but all use the amino acid selenocysteine (Sec), often present in the enzyme's active site. Only about half of mammalian selenoproteins have been functionally characterized, with most being oxidoreductases. The cellular role of selenoprotein T (SelT), manifesting a CxxU motif in a thioredoxin-like fold and localized to Golgi and the endoplasmic reticulum, is not known. To examine its biological funct ...[more]

PMID: 19935881

Similar Datasets

SelT knockdown mouse fibroblast cells vs control cells

Project description:Analysis of gene expression in NIH 3T3 cells stably knockdown for Selt (GenBank accession number NM_001040396) using vector based siRNA technique in comparison to gene expression of vector transfected NIH 3T3 cells.

2009-11-01 | GSE17087 | GEO

UNG shapes the specifity of AID-induced somatic hypermutation in non B cells

Project description:Secondary diversification of antibodies through somatic hypermutation (SHM) and class switch recombination (CSR) is a critical component of the immune response. Activation-induced deaminase (AID) initiates both processes by deaminating cytosine residues in immunoglobulin genes. The resulting U:G mismatch can be processed by alternative pathways to give rise to a mutation (SHM) or a DNA double-strand break (CSR). Central to this processing is the activity of uracil-N-glycosylase (UNG), an enzyme normally involved in error-free base excision repair. We used next generation sequencing to analyze the contribution of UNG to the resolution of AID-induced lesions. Loss- and gain-of-function experiments showed that UNG activity can promote both error-prone and high fidelity repair of U:G lesions. Unexpectedly, the balance between these alternative outcomes was influenced by the sequence context of the deaminated cytosine, with individual hotspots exhibiting higher susceptibility to UNG-triggered error-free or error-prone resolution. These results reveal UNG as a new molecular layer that shapes the specificity of AID-induced mutations and may provide new insights into the role of AID in cancer development. Next Generation Sequencing analysis of mutations introduced by AID in non B cells. NIH-3T3 cells were co-transduced with mOrangeSTOP and AID-ERM-bM-^@M-^Sexpressing vectors, together with Ugi (UNG inhibitor), UNG, or empty vector as control (n=3). Transduced cells were cultured in the presence of OHT during 11 d. AID-E58Q-ER vector (catalytically inactive form of AID) was used as a negative control in combination with the previously described constructions (n=3).

2012-07-04 | E-GEOD-39108 | biostudies-arrayexpress

Examination of the function of NtMYBGR1 and NtDC1B in tobacco BY-2 cells.

Project description:Overexpression lines for each of NtMYBGR1 (Genbank accession No. AB279612) and NtDC1B (Genbank accession No. AB279614) were used to characterize the function of NtMYBGR1 and NtDC1B in tobacco BY-2 cells. We then analyzed the effect of overexpression of these genes on the expression of other genes, using the tobacco microarray. As control sample, tobacco cells transformed with empty vector pMAT137 vector were used. Two control and two transgenic cell lines were analyzed at day 4 after subculture into fresh media. Keywords: Genetic modification

2007-10-16 | GSE6949 | GEO

Sequencing data for single cells and DNA-functionalized microbeads encapsulated in hydrogel droplets.

Project description:DNA barcodes can be used to identify single cells in a sequencing data space while optical codes can be used to track single live cells in an image data space. We have developed dual image and DNA (ID)-coding, which identifies individual single cells in both live image and sequencing data spaces. Samples provided here are relevant to proof-of-concept studies of ID-coding presented in the associated publication. DNA barcoded micro-particles were encapsulated in hydrogel droplets with or without single cells. The hydrogel droplets were then subjected to “single-droplet sequencing” where whole polyA-bearing nucleic acid components within a hydrogel droplet (i.e. mRNA from cells and synthetic DNA on beads) were concatenated by the same cell barcodes.

2023-12-11 | E-MTAB-12988 | biostudies-arrayexpress

Examination of the function of NtMYBGR1 and NtDC1B in tobacco BY-2 cells.

2007-10-15 | E-GEOD-6949 | biostudies-arrayexpress

Influence of C/EBPβ 3'UTR on RasV12 induced gene expression

Project description:C/EBPb is an auto-repressed protein that becomes posttranslationally activated by Ras-MEK-ERK signalling. C/EBPb is required for oncogene-induced senescence (OIS) of primary fibroblasts, but also displays pro-oncogenic functions in many tumour cells. Here, we show that C/EBPb activation by H-RasV12 is suppressed in immortalized/transformed cells, but not in primary cells, by its 30 untranslated region (30UTR). 30UTR sequences inhibited Ras-induced cytostatic activity of C/EBPb, DNA binding, transactivation, phosphorylation, and homodimerization, without significantly affecting protein expression. The 30UTR suppressed induction of senescence-associated C/EBPb target genes, while promoting expression of genes linked to cancers and TGFb signalling. An AU-rich element (ARE) and its cognate RNA-binding protein, HuR, were required for 30UTR inhibition. These components also excluded the Cebpb mRNA from a perinuclear cytoplasmic region that contains activated ERK1/2, indicating that the site of C/EBPb translation controls de-repression by Ras signalling. Notably, 30UTR inhibition and Cebpb mRNA compartmentalization were absent in primary fibroblasts, allowing Ras-induced C/EBPb activation and OIS to proceed. Our findings reveal a novel mechanism whereby non-coding mRNA sequences selectively regulate C/EBPb activity and suppress its anti-oncogenic functions. NIH-3T3 cells were retrovirally infected and selected with appropriate antiobiotics. Equal number of cells were plated and collected 48-72 hours later.

2011-07-22 | E-GEOD-30834 | biostudies-arrayexpress

Transcription profiling of human cholangiocarcinoma cells (cholangiocytes) expressing IL-6

Project description:The association between chronic inflammation and the development and progression of malignancy is exemplified in the biliary tract where persistent inflammation strongly predisposes to cholangiocarcinoma. The inflammatory cytokine interleukin-6 (IL-6) enhances tumor growth in cholangiocarcinoma by altered gene expression via autocrine mechanisms. We therefore investigated the effect of chronic exposure to IL-6 on gene expression using malignant cholangiocytes stably transfected to overexpress IL-6. Comparison of gene expression identified several genes that were altered by enforced IL-6 expression. Experiment Overall Design: Mz-ChA-1 cells were stably transfected with a pTarget vector plasmid containing full length IL-6 under the control of a CMV promoter to generate Mz-IL6. Cells transfected with empty vector were used as control

2008-10-21 | E-GEOD-11883 | biostudies-arrayexpress

Transcription profiling of NIH3T3 cells over-expressing PPARg or EBF1 to study the efficiency and kinetics of cell adipogenesis induced by PPARg and EBF1.

Project description:NIH-3T3 cells transduced with either EBF1-, PPARg2- or empty vector were stimulated with hormones to initiate adipocyte differentiation. RNA extraction was done using TriZol at d0, d2, d4 and d10 after stimulation. Samples were handled according to standard affymetrix protocols. Keywords = Adipogenesis, early B-cell factor 1 (EBF1), commitment, differentiation, NIH-3T3, pparg

2007-09-22 | E-GEOD-2192 | biostudies-arrayexpress

UNG shapes the specificity of AID-induced somatic hypermutation

Project description:This SuperSeries is composed of the following subset Series: GSE39108: UNG shapes the specifity of AID-induced somatic hypermutation in non B cells GSE39114: UNG shapes the specifity of AID-induced somatic hypermutation in B cells Refer to individual Series

2012-07-04 | E-GEOD-39115 | biostudies-arrayexpress

Small RNA-seq of MERS-CoV

Project description:MERS-CoV genome-derived small RNAs in Huh7 cells infected with a Korean isolate of MERS-CoV (KNIH002; Genbank accession no. KT029139.1)

2023-04-17 | GSE148860 | GEO

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