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Fip1 iCLIP-seq in Hela cells without treatment or treated with NC ASO, snoRD50a ASO

ABSTRACT: Fip1 iCLIP-seq in Hela cells without treatment or treated with NC ASO, snoRD50a ASO

PROVIDER: PRJEB19336 | ENA |

REPOSITORIES: ENA

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Fip1 iCLIP-seq in Hela cells without treatment or treated with NC ASO, snoRD50a ASO

Project description:We aimed to compare the Fip1/RNA interaction at transcriptomic level upon snoRD50a knockdown. To this goal, we utilized Fip1 iCLIP-seq protocol in both control and snoRD50a KD hela cells.

2017-07-01 | GSE98220 | GEO

Fip1 iCLIP-seq in Hela cells without treatment or treated with negative control anti-sense oligos (ASO) or snoRD50a ASO to study how snoRD50a affects Fip1/RNA interaction in mRNA 3' processing

Project description:We aimed to discover trans-acting RNA molecules involved in mRNA 3 processing. We reasoned that, if there exist such functional RNAs, they must directly associate with the key machinery responsible for mRNA 3 processing. Therefore, it would be of great value to comprehensively identify RNAs interacting with pre-mRNA 3 processing complex. To this goal, we took advantage of previously well-characterized system combined with high-throughput sequencing to investigate the target RNAs at the transcriptomic level. Fip1 protein is an essential mRNA 3' processing factor. Our in vitro data suggested that snoRD50a affects Fip1/RNA interaction in SV40 late (SVL) polyA site 3' processing. To determine whether snoRD50a influences Fip1/RNA interaction at transcriptomic level in vitro, we performed Fip1 iCLIP-seq experiments in Hela cells transfected with control NC ASO (negative control anti-sense DNA) or snoRD50a ASO.

2017-06-01 | E-MTAB-5384 | biostudies-arrayexpress

PolyA site sequencing (PAS-seq) analysis of Hela cells treated with NC ASO or snoRD50a ASOs

Project description:Our RNA-seq experiment and subsequent in vitro analysis suggested that snoRD50a is a trans-acting RNA that can function in mRNA 3' processing. To test this hypothesis at transcriptomic level, we performed PAS-seq experiments to compare the polyA+ transcripts profile between negative control ASO (nc ASO) and snoRD50a ASO treated Hela cells

2017-07-01 | GSE98219 | GEO

polyA site sequencing (PAS-seq) analysis of Hela cells treated with NC ASO or snoRD50a ASOs

Project description:Our RNA-seq experiment (E-MTAB-5383) and subsequent in vitro analysis suggested that snoRD50a is a trans-acting RNA that can function in mRNA 3' processing. To test this hypothesis at transcriptomic level, we performed PAS-seq experiments to compare the polyA+ transcripts profile between negative control ASO (nc ASO) and snoRD50a ASO treated Hela cells, ASO (antisense oligonucletode) technique is a commonly used technique to deplete nuclear RNAs. snoRD50a ASO is used to deplete endogenous snoRD50a. See related experiments: E-MTAB-5383; E-MTAB-5384.

2017-05-31 | E-MTAB-5389 | biostudies-arrayexpress

Homo sapiens

Project description:Fip1 iCLIP-seq in Hela cells without treatment or treated with NC ASO, snoRD50a ASO

| PRJNA384325 | ENA

HTS-Seq analysis of Hela cells treated with NC ASO or snoRD50a ASOs

Project description:HTS-Seq analysis of Hela cells treated with NC ASO or snoRD50a ASOs

| PRJNA384322 | ENA

polyA site sequencing (PAS-seq) analysis of Hela cells treated with NC ASO or snoRD50a ASOs

Project description:polyA site sequencing (PAS-seq) analysis of Hela cells treated with NC ASO or snoRD50a ASOs

| PRJEB19851 | ENA

RNA-seq analysis of HeLa cells following MYC inhibition with ASO

Project description:We performed RNA-seq on HeLa cells treated with MYCASO-3, a non-targeting ASO (NT-ASO), Lipofectamine alone, and untreated cells

2021-10-19 | GSE183535 | GEO

iCLIP of HeLa cells with anti-TFIP11 antibody

Project description:iCLIP of HeLa cells with anti-TFIP11 antibody to investigate RNA binding locations of TFIP11 as part of a larger study on the function of TFIP11.

2021-09-22 | GSE158589 | GEO

iCLIP of eIF4A3 and PTB in HeLa cells

Project description:HeLa cells were cultured in DMEM, supplemented with 10% (v/v) FCS and penicillin/streptomycin under 5% CO2 at 37°C. For iCLIP, HeLa cells expressing eIF4A3-GFP or PTB-GFP were induced with doxycycline to adjust the level of recombinant protein to the level of the endogenous counterpart and irradiated with 150 mJ/cm2 UV light (254 nm). The iCLIP cDNA libraries for eIF4A3 and PTB were sequenced with 50 bp on an Illumina HiSeq instrument.

2015-08-11 | E-MTAB-2599 | biostudies-arrayexpress

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