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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The splicing activator DAZAP1 integrates splicing control into MEK/Erk regulated cell proliferation and migration

ABSTRACT: DAZAP1 was depleted in culterd HEK 293T cells using shRNA and the resulting poly A RNA were isolated c-DNA library constructed and paired end sequenced on illumina Hi-seq 2000 platform the data was compared to a control shRNA depleted cell Gene expression and splicing switches upon DAZAP1 knockdown

ORGANISM(S): Homo sapiens

SUBMITTER: Zefeng Wang

PROVIDER: E-GEOD-52745 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The splicing activator DAZAP1 integrates splicing control into MEK/Erk regulated cell proliferation and migration

Project description:DAZAP1 was depleted in culterd HEK 293T cells using shRNA and the resulting poly A RNA were isolated c-DNA library constructed and paired end sequenced on illumina Hi-seq 2000 platform the data was compared to a control shRNA depleted cell

2013-12-25 | GSE52745 | GEO

The splicing activator DAZAP1 integrates splicing control into MEK/Erk-regulated cell proliferation and migration.

Project description: Not available

| S-EPMC4146490 | biostudies-literature

The splicing factor RBM4 controls apoptosis, proliferation, and migration to suppress tumor progression

Project description:Gene expression and splicing switches upon RBM4 overexpression 2 Samples

2014-09-18 | E-GEOD-58594 | biostudies-arrayexpress

Human Cactin interacts with DHX8 and SRRM2 to assure efficient pre-mRNA splicing and sister chromatid cohesion.

Project description:We analysed whole PolyA+ RNA from human osteosarcoma U2OS cells depleted for human Cactin or transfected with a control shRNA. Two independent shRNAs targeting human Cactin (shCac_C and shCac_D), a control shRNA (shCtrl), a single cell line (U2OS)

2016-06-01 | E-GEOD-82070 | biostudies-arrayexpress

Sub-genomewide shRNAs constructed using an optimized selection algorithm and microRNA backbone provide stronger evidence for follow-up studies

Project description:Sub-genomewide shRNA libraries were constructed using the current RNAi consortium constructs as well as using the DSIR (siRNA algoirthm) and a novel shRNA specific algorithm (shERWOOD). All libraries were placed into mir30 expression vectors. The shERWOOD libraries were also placed in a vector harboring an optimized mir cassette (ultramir). Each library was screened using the pancreatic cell line A385. A concensus set of essential genes identified as the set for which two shRNAs depleted in each of the libries. For these genes, a great percentage of shERWOOD seletected shRNA depleted. In addition the placement of shERWOOD selected constructs into ultramir scaffoled increased the rate of shRNA depletion for essential genes further. Purpose: shRNA screens were carried out using various library construction strategies to identify the strategy that provides the best shRNA screening results. Method: Libraries were constructed using the TRC shRNA set as well as shRNAs identified using the DSIR and shERWOOD algorithms. shRNA libraries were cloned into mir30 expression vectors. shERWOOD shRNAs were also cloned into an expression vector harboring an optimized microRNA scaffold termed ultramir. Each resultant library was screened using the pancreatic cell line A385. Each library was analyzed separately to identify a set of genes where at least two shRNAs depleted. These gene sets were intersected to develop a set of essential genes. Results: The shERWOOD shRNA libraries provided the highest number depleting shRNAs for each essential gene. Further these shRNAs depleted to a greater extent than did the shRNAs from the other libraries. When shERWOOD libraries were placed into the ultramir cassette a greater number of shRNAs per essential gene depleted.

2014-11-24 | E-GEOD-62185 | biostudies-arrayexpress

Loss of nuclear TDP-43 in ALS causes altered expression of splicing machinery and widespread dysregulation of RNA splicing in motor neurons [NSC34]

Project description:Aims: Loss of nuclear TDP-43 characterises sporadic and most familial forms of amyotrophic lateral sclerosis (ALS). TDP-43 (encoded by TARDBP) has multiple roles in RNA processing. We aimed to determine whether 1) RNA splicing dysregulation is present in lower motor neurons in ALS and in a motor neuron-like cell model, and 2) TARDBP mutations (mtTARDBP) are associated with aberrant RNA splicing using patient-derived fibroblasts. Methods: Affymetrix exon arrays were used to study mRNA expression and splicing in lower motor neurons obtained by laser capture microdissection of autopsy tissue from individuals with sporadic ALS and TDP-43 proteinopathy. Findings were confirmed by qRT-PCR and in NSC34 motor neuronal cells following shRNA-mediated TDP-43 depletion. Exon arrays and immunohistochemistry were used to study mRNA splicing and TDP-43 expression in fibroblasts from patients with mtTARDBP-associated, sporadic and mutant SOD1-associated ALS. Results: We found altered expression of spliceosome components in motor neurons and widespread aberrations of mRNA splicing that specifically affected genes involved in ribonucleotide binding. This was confirmed in TDP-43 depleted NSC34 cells. Fibroblasts with mtTARDBP showed loss of nuclear TDP-43 protein and demonstrated similar changes in splicing and gene expression, that were not present in fibroblasts from patients with sporadic or SOD1-related ALS. Conclusion: Loss of nuclear TDP-43 is associated with RNA processing abnormalities in ALS motor neurons, patient-derived cells with mtTARDBP, and following artificial TDP-43 depletion, suggesting that splicing dysregulation directly contributes to disease pathogenesis. Key functional pathways affected include those central to RNA metabolism. RNA was extracted from NSC34 motor neuronal cells depleted of TDP-43 by shRNA (n=4), treated with control shGFP (n=4), and treated with control shLuciferase (n=3).

2014-06-01 | E-GEOD-56503 | biostudies-arrayexpress

Role of 4EBP1/2 in the response to glucose deprivation

Project description:We investigated the function of the mTORC1 substrates and mRNA translation regulators 4EBP1/2 in the response to glucose deprivation. We uncovered that targeting 4EBP1/2 expression had a direct impact on the survival rates of cells challenged with glucose deprivation. To further define the mechanisms underlying 4EBP1/2 function under glucose deprivation, we conducted a proteomics analysis of HEK293 shRNA control and HEK293 shRNA 4EBP1/2 grown in basal media or under glucose deprivation (1 mM glucose containing media) for 30 hours.

2024-03-28 | PXD040931 | Pride

Identification of Zdhhc20 knock-down cell palmitome

Project description:An shRNA screen to search for the mediators of pancreatic cancer metastasis identified palmitoyl transferase ZDHHC20 as a protein that mediates this process by promoting the outgrowth of metastatic cells in vivo. We sought to identify the changes in the palmitome of the cells expessing scrambled shRNA or shRNAs targeting Zdhhc20.

2023-02-09 | PXD038048 | Pride

RNAi expression experiments on Illumina BeadChip

Project description:Mouse embryonic stem cells (mES) were depleted of Klf2, Klf4, and Klf5 by ectopic expression of shRNA. Control RNAi was performed using shRNA against luciferase. At 2 days, 4 days and 6 days post-transfection of shRNA-encoding vectors, cells are harvested for RNA isolation. Keywords: RNAi expression, Mouse ES cells Knockdown: Klf2, Klf4, Klf5, Luciferase (Control);Time: 2 days post-transfection, 4 days post-transfection, 6 days post-transfection;Three independent experimental replicates for each experimental condition were performed.

2010-06-25 | E-GEOD-9775 | biostudies-arrayexpress

Gene expression analysis of untreated and NT-shRNA transduced kidney proximal tubular epithelial cells (PTECs) at day 6 and day 16 after transduction, as well as SETD2-shRNA transduced PTECs at day 25 after transduction.

Project description:Primary kidney PTECs gradually became senescesince day 16, but SETD2 depletion prevented PTECs from senescence and maintained their proliferation beyond their limited dividing capacity. Transcriptional profiling of human PTECs, with comparing of non-senescent PTECs (PTECs-day 6), senescent PTECs (PTECs-day16), and SETD2 depleted PTECs at day 25 (SETD2 KD-PTECs-day 25). Three PTECs of different origins were transduced with shRNA constructs against SETD2 (sh1 or sh2), or with a non-targeting sequence. Untreated and NT-shRNA transduced samples were harvest at day 6 and day 16 respectively, SETD2-KD shRNA transduced PTECs were harvest at day 25.

2016-01-09 | E-GEOD-72792 | biostudies-arrayexpress

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