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The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.

The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background.

Authors :
Ducoli L
Agrawal S
Hon CC
Ramilowski JA
Sibler E
Tagami M
Itoh M
Kondo N
Abugessaisa I
Hasegawa A
Kasukawa T
Suzuki H
Carninci P
Shin JW
de Hoon MJL
Detmar M
Source :
BMC genomic data [BMC Genom Data] 2021 Sep 14; Vol. 22 (1), pp. 33. Date of Electronic Publication: 2021 Sep 14.
Publication Year :
2021

Abstract

Background: The lymphatic and the blood vasculature are closely related systems that collaborate to ensure the organism's physiological function. Despite their common developmental origin, they present distinct functional fates in adulthood that rely on robust lineage-specific regulatory programs. The recent technological boost in sequencing approaches unveiled long noncoding RNAs (lncRNAs) as prominent regulatory players of various gene expression levels in a cell-type-specific manner.<br />Results: To investigate the potential roles of lncRNAs in vascular biology, we performed antisense oligonucleotide (ASO) knockdowns of lncRNA candidates specifically expressed either in human lymphatic or blood vascular endothelial cells (LECs or BECs) followed by Cap Analysis of Gene Expression (CAGE-Seq). Here, we describe the quality control steps adopted in our analysis pipeline before determining the knockdown effects of three ASOs per lncRNA target on the LEC or BEC transcriptomes. In this regard, we especially observed that the choice of negative control ASOs can dramatically impact the conclusions drawn from the analysis depending on the cellular background.<br />Conclusion: In conclusion, the comparison of negative control ASO effects on the targeted cell type transcriptomes highlights the essential need to select a proper control set of multiple negative control ASO based on the investigated cell types.<br /> (© 2021. The Author(s).)

Details

Language :
English
ISSN :
2730-6844
Volume :
22
Issue :
1
Database :
MEDLINE
Journal :
BMC genomic data
Publication Type :
Academic Journal
Accession number :
34521352
Full Text :
https://doi.org/10.1186/s12863-021-00992-1