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

Posted on 15.09.2021 - 03:22
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. 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. 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.

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Ducoli, Luca; Agrawal, Saumya; Hon, Chung-Chau; Ramilowski, Jordan A.; Sibler, Eliane; Tagami, Michihira; et al. (2021): The choice of negative control antisense oligonucleotides dramatically impacts downstream analysis depending on the cellular background. figshare. Collection. https://doi.org/10.6084/m9.figshare.c.5618809.v1
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BMC Genetics

AUTHORS (16)

Luca Ducoli
Saumya Agrawal
Chung-Chau Hon
Jordan A. Ramilowski
Eliane Sibler
Michihira Tagami
Masayoshi Itoh
Naoto Kondo
Imad Abugessaisa
Akira Hasegawa
Takeya Kasukawa
Harukazu Suzuki
Piero Carninci
Jay W. Shin
Michiel J. L. de Hoon
Michael Detmar

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