Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: RNA-sequencing of B-ALL cell lines, REH treated with LNA GapmeRs against four lncRNAs

PROVIDER: PRJNA317295 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3330020.fastq.gz	Fastqsanger.gz
	SRR3330030.fastq.gz	Fastqsanger.gz
	SRR3330040.fastq.gz	Fastqsanger.gz
	SRR3330021.fastq.gz	Fastqsanger.gz
	SRR3330031.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 27

Similar Datasets

RNA-seq to investigate gene expression profile associated with long-non coding RNA RAIN in TPC1 cells

Project description:We used RNA-seq analysis to identify gene expression profile in TPC1 cells transfected with LNA gapmers against RAIN vs control

2018-09-01 | E-MTAB-6622 | biostudies-arrayexpress

Gene expression analysis in liver collected from mice administered non-toxic, toxic, or severely toxic LNA sequences

2014-01-08 | GSE53230 | GEO

Illumina Microarray of T47D cell with or without KDM7A-DT silencing under normal and oxidative stress conditions

Project description:KDM7A Divergent Transcript (KDM7A-DT) is a stress-induced lncRNAs. In our previous studies, KDM7A-DT showed the most robust cellular phenotype alteration and a significant TP53-dependency upon oxidative and oncogenic stress induction. Since about 50% of human breast cancers have mutant p53 and associated genetic alterations, it is essential to determine what effect a mutant p53 would have on acquired pro-oncogenic functions of KDM7A-DT. In these experiments, we used four antisense LNA Gapmer sequences designed by Exiqon (Vedbaek, Denmark). One of these was a negative control, while the other 3 were designed to target the end of the transcript representing the full-length lncRNA KDM7A-DT (lncRNA; GRCh38/hg38, chr7: 140,178,951-140,179,640). To test the effect of KDM7-DT in the context of mutant p53, we selected the p53-negative luminal BC cells T47D. For each of the LNA gapmers, we utilized 3 technical replicates across two main experimental conditions (normal vs. oxidative stress induced via 30 mins of 0.2 mM H2O2 treatment). Overall, we measured the signals for 47,323 Illumina array probes across 24 individual experiments (4 LNA gapmers * 3 technical replicates * 2 main experimental conditions).

2023-05-01 | E-MTAB-11818 | biostudies-arrayexpress

Gene expression analysis in liver collected from mice administered non-toxic, toxic, or severely toxic LNA sequences

Project description:Development of LNA gapmers, antisense oligonucleotides used for efficient inhibition of target RNA expression, is limited by non-target mediated hepatotoxicity issues. In the present study, we investigated hepatic transcription profiles of mice receiving non-toxic and toxic LNA gapmers after a single and repeat administration. To understand the mechanism of LNA gapmer-induced heptotoxicity in mice, we investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1), toxic sequence (TS-2), or severely toxic sequence (HTS-3) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 8, 16, or 72 hrs after a single administration (by subcutaneous injection ) using microarray analysis. We also investigated the transcription profiles of liver RNA isolated from mice receiving non-toxic sequence (NTS-1) or toxic sequence (TS-2) of LNA gapmers at 25 mg/kg (dose volume of 10 mL/kg) at 2 weeks after repeated administration (by subcutaneous injection ) using microarray analysis.

2014-01-08 | E-GEOD-53230 | biostudies-arrayexpress

Proteomic profile of human breast cancer cells expressing normal levels or absent of the long non-coding RNA NORAD.

Project description:We describe here the proteome of the human breast cancer cell line MDA-MB-231 expressing normal levels of the lncRNA NORAD, or after knock-down NORAD with siRNA and LNA gapmers.

2023-08-28 | PXD039920 | Pride

H3K27ac ChIP-Seq in REH and 697

Project description:H3K27ac ChIP-Seq data of the B-ALL cell lines REH and 697 were obtained to find active regions in the genome and to correlate that with expression profiling of lncRNAs in these cell lines.

2016-09-26 | GSE79870 | GEO

Cisplatin-inducible death receptor 5 antisense long non-coding RNA modulates cell cycle and proliferation in HeLa cells

Project description:We have performed a transcriptomics study in which we first transfected LNA GapmeRs against DR5-AS lncRNA to silence it in HeLa cells. Total RNA was isolated from control as well as transfected cells and silencing was confirmed by qPCR. Total RNAs were subjected to deep-sequencing to identify differentially expressed mRNAs. We then took advantage of bioinformatic tools to identify which pathways are affected by DR5-AS knock-down.

2021-04-01 | GSE160227 | GEO

Total paired-end RNA sequencing of bone marrow and peripheral blood MNCs from patients with Juvenile myelomonocytic leukemia and age-matched controls

Project description:Dysregulation of the non-coding RNA transcriptome has been demonstrated in Juvenile myelomonocytic leukemia (JMML), a rare and aggressive disorder of early childhood. Currently, JMML treatment relies on hematopoietic stem cell transplantation resulting in long-term overall survival of only 50-60%. Consequently, there is need to develop novel treatments. In this study we investigated the therapeutic potential of targeting overexpressed long non-coding RNAs (lncRNAs) in JMML. Total RNA sequencing from 19 previously untreated JMML patients and 3 pediatric normal bone marrow samples revealed 202 differentially expressed lncRNA genes (144 upregulated and 58 downregulated). Molecular knockdown (≥ 70% compared to mock control) after 24h of incubation was observed for 6 out of 10 overexpressed lncRNAs for which LNA GapmeRs were designed. For 3 lncRNAs (lnc-THADA-4-1, lnc-ACOT9-1 and NRIR) knockdown resulted in a significant effect on cell viability after 96h or 72h of incubation in cell lines or in primary JMML cells, respectively. Importantly, the extend of cellular damage correlated well with the expression of the lncRNA of interest. In conclusion, we provided proof-of-concept that knockdown of overexpressed lncRNAs such as lnc-THADA-4-1, lnc-ACOT9-1 and NRIR is a feasible therapeutic strategy in vitro in haematopoietic cell lines and in primary JMML cells. These results will need further validation in JMML xenograft models.

2021-01-27 | GSE147523 | GEO

Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL [ANRIL_LNA_Affy]

Project description:To identify the genes differentially expressed upon the knockdown of the lncRNA ANRIL using LNA GapmeRs in HEK293 cells

2021-05-26 | GSE162223 | GEO

RNAseq of Breast Implanted ALK-negative anaplastic large cell lymphoma cell line (TLBR2) upon silencing of a novel lncRNA specifically associated with the ALK-negative anaplastic large cell lymphomas.

Project description:Identification of transcriptional program influenced by the expression of lncRNA MAAT, a novel lncRNA highly expressed and strongly correlated with ALK-negative anaplastic large cell lymphomas. LncRNA MAAT was silenced through Antisense LNA GapmeRs strategy.

2024-12-13 | E-MTAB-12462 | biostudies-arrayexpress

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