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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Expression data from HeLa cells overexpressing AK125393

ABSTRACT: Expression of RAD51, a crucial player in homologous recombination (HR) and DNA double-strand break (DSB) repair, is dysregulated in human tumors, and can contribute to genomic instability and tumor progression. To further understand RAD51 regulation we functionally characterized a long non-coding (lnc) RNA, AK125393, dubbed TODRA (Transcribed in the Opposite Direction of RAD51), transcribed 69bp upstream to RAD51, in the opposite direction. TODRA overexpression in HeLa cells induced expression of TPIP, a member of the TPTE family which includes PTEN. Similar to PTEN, we found that TPIP co-activates E2F1 induction of RAD51. HeLa cells were transfected with either an empty vector or an AK1253893 minigene. RNA was extracted from duplicates of each experiment and hybridized to affymetrix microarray.

ORGANISM(S): Homo sapiens

SUBMITTER: Sharon Zeligson

PROVIDER: E-GEOD-66062 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Expression data from HeLa cells overexpressing AK125393

Project description:Expression of RAD51, a crucial player in homologous recombination (HR) and DNA double-strand break (DSB) repair, is dysregulated in human tumors, and can contribute to genomic instability and tumor progression. To further understand RAD51 regulation we functionally characterized a long non-coding (lnc) RNA, AK125393, dubbed TODRA (Transcribed in the Opposite Direction of RAD51), transcribed 69bp upstream to RAD51, in the opposite direction. TODRA overexpression in HeLa cells induced expression of TPIP, a member of the TPTE family which includes PTEN. Similar to PTEN, we found that TPIP co-activates E2F1 induction of RAD51.

2015-02-19 | GSE66062 | GEO

RNA-seq of human cell line HeLa after depletion of a lncRNA with three different loss-of-function methods

Project description:Long noncoding RNAs (lncRNAs) are a major transcriptional output of the mammalian genome, and their cellular roles are typically assayed by a variety of loss-of-function approaches. This study aims to identify the best current method to deplete nuclear lncRNAs. Small interfering RNAs (RNAi), antisense oligonucleotides (LNAs) and CRISPR interference (CRISPRi) were applied to knock down loc100289019 (a typical nuclear lncRNA, referred to as lnc289) in HeLa cells. We generated sequencing libraries after performing each step of each method, up to and including depletion of lnc289. Differential expression analyses between libraries generated before and after each step allowed us to evaluate the effect of that step on gene expression. The transcriptional effect of lncRNA depletion was then compared to the magnitude of off-target effects inherent to each method.

2017-05-31 | E-MTAB-5308 | biostudies-arrayexpress

Regulation of transcription by HIPPI and its molecular partner HIP1

Project description:This SuperSeries is composed of the following subset Series: GSE26115: Regulation of transcription by HIP1 protein interactor (HIPPI) in HeLa cells GSE26116: Role of HIP1 in HIPPI mediated transcription regulation in HeLa cells Refer to individual Series

2011-09-20 | E-GEOD-26117 | biostudies-arrayexpress

SF3b155 knock-down by two different siRNA oligos in HeLa cells

Project description:Analysis of the alternative pre-mRNA procesing after SF3b155 siRNA knock-down in HeLa cells employing a custom microarray platform sensitive to splicing. HeLa cells were transfected with either a scrambled RNA or one of the two different SF3b155 siRNA oligonucleotides (oligo 3: 5’-GACAGCAGAUUUGCUGGAUACGUGA-3; oligo 5: 5’-CCCUGUGGCAUUGCUUAAUGAUAU-3’). Total RNA samples from three biological replicates were labeled in direct and dye-swap hybridizations. Labeled samples were hybridized into our custom splicing-sensitive agilent platform which contains 1804 splicing events from 482 genes.

2011-03-08 | E-GEOD-22952 | biostudies-arrayexpress

Transcriptomic profiling of HeLa cells treated with miR-15a, miR-16, miR-503 and control-miR

Project description:To have a global picture of the targets of the miR-15 family, we assessed transcriptome changes, by deep-sequencing, of HeLa cells transfected with 3 members of the miR-15 family (miR-15a, miR-16 or miR-503) or a control miRNA (cel-miR-231). We observed a very extensive overlap between the genes down-regulated by these 3 miRNAs, as expected for miRNAs belonging to the same family. transcriptmic profiles of HeLa cells treated miR-15a, miR-16, miR-503 and control-miR were generated by deep sequencing, using Illumina HiSeq2000.

2014-07-18 | E-GEOD-53279 | biostudies-arrayexpress

Exon array expression profiling: DYRK1A acts as transcriptional activator

Project description:Transcriptome analysis of depletion of DYRK1A in HeLa cells Global gene expression profiling has shown upregulation of many genes in the context of DYRK1A depletion in HeLa cells. Many of these genes deregulated by DYRK1A are involved in immune response system. Transcriptome analysis of siRNA against DYRK1A transfected in HeLa cells on GeneChipM-BM-. Human Exon 1.0 ST Arrays (Affimetrix). Control HeLa cells have been transfected with the same concentration of siRNA non-targeting (siNT). Experiment has been done experimental triplicates.

2014-05-01 | E-GEOD-43259 | biostudies-arrayexpress

Genome-wide effect of Galectin-7 ectopic expression in HeLa and SiHa cervical cancer cell lines.

Project description:The Galectin-7 gene has been found subregulated in several cervical cancer cell lines and in clinical samples. To study the changes in the cell system after the ectopic expression of Galectin-7, we used microarrays to analyze transcriptome of HeLa and SiHa cancer cell line. Cells were transfected with a viral vector with the Galectin-7 gene and negative controls in 3 biological replicates and analyzed to study gene expression changes. Array data from the same study has also been deposited at ArrayExpress under accession number E-MTAB-3307 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3307/) and E-MTAB-3308 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3308/)

2016-03-01 | E-MTAB-3306 | biostudies-arrayexpress

Role of HIP1 in HIPPI mediated transcription regulation in HeLa cells

Project description:Nuclear entry of transcription factor HIPPI is mediated by its interacting partner Huntingtin Interacting Protein 1 (HIP1), a nuclear localization signal containing nucleo-cytoplasmic shuttling protein. In oredr to investigate the role of HIP1 in HIPPI mediated transcriptional regulation in cell, here we performed microarray experiments using stable HIP1 knocked down HeLa cells (Hip1Si) exogenously expressing Green fluorescent protein tagged HIPPI. Total RNA extracted from HIP1 knocked down HeLa cells (Hip1Si) transfected with empty GFP vector served as control and Total RNA extracted from Hip1Si cells transfected with GFP-Hippi construct served as test. Biological replicates: 4

2011-09-20 | E-GEOD-26116 | biostudies-arrayexpress

Gene silencing of BSK65-MONO1 (RNF185) and of its natural antisense RNA (RNF185-AS) using siRNAs

Project description:Microarray profiles of native HeLa cells and RNF185/BSK65 gene silenced HeLa cells using siRNAs LMG2 and LMG4 were monitored using Affymetrix U133 Plus 2.0 microarrays. Two independent microarray assays of each analysis were used for the comparison of native vs. siRNA treated HeLa cells with LMG2 and LMG4.

2013-06-07 | E-GEOD-47685 | biostudies-arrayexpress

ASF1

Project description:Transcription profiling by array of HeLa cells after the knock-down of ASF1 (ASF1a & ASF1b) by siRNA compared to non-targeting control siRNA

2014-01-14 | E-MTAB-1909 | biostudies-arrayexpress

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