Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

39 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Cheng Guo Yao

PROVIDER: E-MTAB-5384 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

HF liver: Control vs. Plin2-ASO treated

Project description:Transcriptional profiling of mouse liver comparing control, scrambled-oligonucleotides (Cont)-treated mice with Perilipin 2-antisense oligonucleotides (Plin2-ASO)-treated mice. C57BL/6 mice on a high-fat diet were treated with oligonucleotides in vivo. The goal was to determine the effects of Plin2 down-regulation in the liver on global gene expression. Two-condition experiment, control oligonucleotides vs. Plin2-antisense oligonucleotides. Biological replicates: 4 control replicates, 4 Plin2-ASO replicates.

2012-12-05 | E-GEOD-37011 | biostudies-arrayexpress

mRNA expression profile in IL-4-treated macrophages transfected with miR-142-5p ASO or miR-130a-3p mimics

Project description:To identify target genes of miR-142-5p and miR-130a-3p that are involved in M2 polarization, we examined the mRNA expression profile changes after altering miR-142-5p or miR-130a-3p expression in IL-4-treated macrophages. Macrophages were transfected with control ASO, miR-142-5p ASO, control mimics or miR-130-3p mimics using lentiviral vectors. After 24 hr, the cells were treated with IL-4 for 24h.mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3’ bias utilizing a random priming method. The labeled cRNAs were hybridized onto the Human RNA Array v2.0 (8 x 60K, Arraystar). After having washed the slides, the arrays were scanned by the Agilent Scanner G2505B.

2014-07-12 | E-GEOD-59347 | biostudies-arrayexpress

Preliminary small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

Project description:Proliferation of tumor cells transfected with ASO-1537S is inhibited compared to controls. The aim of the experiment is to determine changes in microRNA expression profiles with treatment, compared to controls.

2023-06-02 | E-MTAB-6762 | biostudies-arrayexpress

Small RNAseq of human breast cancer cell line MDA-MB-231 transfected with antisense oligonucleotide 1537S (ASO-1537S), compared to control oligonucleotide (ASO-C) and untreated cells

2023-06-02 | E-MTAB-6768 | biostudies-arrayexpress

HIPSTR lncRNA knockdown in H1BP cells

Project description:HIPSTR is a conserved lncRNA that is transcribed antisense to TFAP2A gene. Unlike previously reported antisense lncRNAs, HIPSTR expression does not correlate with the expression of its antisense counterpart. HIPSTR depletion in HEK293 and H1BP cells predominantly affects genes involved in early organismal development and cell differentiation. H1BP cells were transfected with antisense oligonucleotides (ASOs) targeting HIPSTR (ASO #0, ASO #1 or ASO #2) or control scrambled ASO (ASO CTL); transfections with each targeting ASO were done in duplicate, transfections with control ASO were done in triplicate.

2016-09-08 | E-GEOD-77936 | biostudies-arrayexpress

HIPSTR lncRNA knockdown in HEK293 cells

Project description:HIPSTR is a conserved lncRNA that is transcribed antisense to TFAP2A gene. Unlike previously reported antisense lncRNAs, HIPSTR expression does not correlate with the expression of its antisense counterpart. HIPSTR depletion in HEK293 and H1BP cells predominantly affects genes involved in early organismal development and cell differentiation. HEK293 cells were transfected with antisense oligonucleotides (ASOs) targeting HIPSTR (ASO #1 or ASO #2) or control scrambled ASO (ASO CTL); transfection with each ASO was done in triplicate.

2016-09-08 | E-GEOD-77935 | biostudies-arrayexpress

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

Targeted degradation of sense and antisense C9orf72 RNA foci as therapy for amyotrophic lateral sclerosis and frontotemporal dementia (strand specific RNA-seq)

Project description:Purpose: The purpose of this experiment is to identify expression changes after ASO-dependent depletion of mouse C9orf72 in the spinal cord of wild-type C57Bl/6 female mice. Methods: Strand specific RNA-seq was performed using RNAs extracted from spinal cord of C57Bl/6 mice two weeks after intracerebroventricular stereotactic injection of saline (n=3), a control ASO (n=3) or an ASO targeting mouse C9orf72 (n=3). C9orf72 RNA levels were reduced to approximately 30% of control levels in spinal cords from mice treated with the C9orf72 ASO. Results: Statistical comparison of RPKM values between RNAs from C9orf72 and control ASO treated animals or C9orf72 and saline treated samples revealed that only 12 genes were consistently upregulated (defined by P<0.05 adjusted for multiple testing) and 12 genes including C9orf72 were downregulated (defined by P<0.05 adjusted for multiple testing). Conclusions: Only few RNA expression changes were identified in the spinal cord following reduction of C9orf72. Use of strand specific RNA-seq to test the consequences of C9orf72 loss of function in mouse spinal cord.

2013-11-12 | E-GEOD-51685 | 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

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data