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Transcriptomic analysis of HeLa cells depleted in CELF1, ELAVL1, and both

ABSTRACT: Transcriptomic analysis of HeLa cells depleted in CELF1, ELAVL1, and both

PROVIDER: PRJNA487606 | ENA |

REPOSITORIES: ENA

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Transcriptomic analysis of HeLa cells depleted in CELF1, ELAVL1, and both

Project description:ELAVL1 and CELF1 are two RNA-binding proteins involved in alternative splicing control. To address their functional relationships, we identify the differentially spliced mRNAs upon depletion of CELF1, ELAVL1, or both. These proteins control similar sets of genes with similar consequences on exon inclusion or skipping. The magnitude of the effect of the double depletion equals the sum of the magnitudes of the individual depletions, showing that CELF1 and ELAVL1 additively control their target RNAs. CELF1 and ELAVL1 regulated splicing events include ACSL4, WNK1, CD44, MICAL3, and JDP2. Using FRET, we find that CELF1 and ELAVL1 directly interact in cell nuclei. We demonstrate that the combined levels of CELF1 and ELAVL1 is a valuable biomarker in breast cancer, while their levels bring very limited information when taken individually. A “co-RNA splicing map” of CELF1 and ELAVL1 shows they repress alternative splice sites when bound nearby, but activate them when bound further away. Together, these data point to strong functional interactions between CELF1 and ELAVL1 to control alternative splicing with significant impacts in human pathology.

2021-08-01 | GSE118981 | GEO

Quantitative Analysis of Transcriptomes between Negative control, UBR5 depleted and MYC depleted HeLa cells

Project description:Purpose: The goal of this study is to compare the transcriptome changes between Negative control, UBR5 depleted and MYC depleted HeLa cells Methods: Gene expression profiles of Negative control, UBR5 depleted and MYC depleted HeLa cells were generated by deep sequencing, in triplicate. Results:The data were analyzed, and we sucessfully detected global differences in the gene expression between the given groups. Conclusions: UBR5 depletion induces gene expression changes that are partly overlapping with gene expression changes induced by MYC depletion

2020-01-15 | GSE143517 | GEO

Gene expression profiling of N-acetylglucosaminidase (NAGLU)-depleted HeLa cells versus non-depleted cells

Project description:We generated a HeLa cell model of mucopolysaccharidosis IIIB (MPSIIIB) by depleting NAGLU. MPSIIIB-associated cell defects were prominent in NAGLU-depleted cells. We explored alterations of metabolic pathways in NAGLU-depleted cells versus non-depleted control cells by performing gene expression profiling. Exon array transcriptome analysis showed 96 transcripts with increased expression level and 38 transcripts with decreased expression level in NAGLU-depleted versus non-depleted cells.

2012-09-13 | GSE32154 | GEO

Gene expression profiling of N-acetylglucosaminidase (NAGLU)-depleted HeLa cells versus non-depleted cells

2012-09-13 | E-GEOD-32154 | biostudies-arrayexpress

Transcriptome analysis of TFAM-depleted HepG2 cells and HeLa cells

Project description:We conducted transcriptome analysis of TFAM-depleted HepG2 cells and HeLa cells as a mitochondrial stress model. We found that mitochondrial dysfunction upregulated unique secretory proteins such as amphiregulin (AREG) and thrombospondin 1 in hepatic cells.

2022-09-28 | GSE196511 | GEO

polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQT)

Project description:The libraries contained in this experiment come from the cytoplasmic fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-12-07 | GSE90255 | GEO

polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQI)

Project description:The libraries contained in this experiment come from the nuclear fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-12-07 | GSE90246 | GEO

Quantitative Analysis of Transcriptomes between Negative control, UBR5 depleted and MYC depleted HeLa cells

Project description:Quantitative Analysis of Transcriptomes between Negative control, UBR5 depleted and MYC depleted HeLa cells

| PRJNA600869 | ENA

polyA depleted RNA-seq from HeLa-S3 (ENCSR000CQJ)

Project description:The libraries contained in this experiment come from the whole cell fraction of independent growths of cell line HeLa-S3. They are stranded PE76 Illumina GAIIx RNA-Seq libraries from rRNA-depleted and DSN normalized Poly-A- RNA > 200 nucleotides in size. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf

2016-12-07 | GSE90247 | GEO

iTRAQ-based quantitative proteomic analysis of nuclear proteome in VPS35-depleted HeLa cells

Project description:Stable VPS35 knockdown HeLa cells were generated using lentiviral short hairpin RNA (shRNA) construct. Isobaric tags for relative and absolute quantitation (iTRAQ)-based mass spectrometry was used to measure the changes of nuclear protein abundance in VPS35-depleted HeLa cells.

2022-08-12 | PXD027166 | Pride

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