Correction to: Cell & Bioscience (2022) 12:84 https://doi.org/10.1186/s13578-022-00804-8
After publication of the original article [1], we realized that two files in the Supplementary Information, Additional files 4 and 7, were incorrect. The correct Additional files 4 and 7 are available on Cell & Bioscience’s website from the date of publication of this note.
In addition, a part of the Methods section was missing in the original article. Methods for Additional file 4 are as follows:
Burrows-Wheeler aligner BWA-MEM 0.7.15 (RRID:SCR_010910) was used to align paired-end reads to the UCSC mouse genome build mm10 with standard settings. Alignments were converted to BAM format and de-duplicated with Picard tools 2.9.0 (RRID:SCR_006525). To quantify relative expression of transcripts, we ran StringTie 1.3.3 (RRID:SCR_016323) [2] and calculated the transcripts per million (TPM) reads. Sample scaling and statistical analyses were performed with the R package edgeR (RRID:SCR_012802) [3]. Transcripts with TPM > 0 in all samples were kept for downstream analysis. Differentially expressed genes with an absolute value of log2 fold change ≥ 1 and a false-discovery rate (FDR) < 0.05 were considered statistically significant.
References
Gutiérrez J, van Wely KHM, Martínez-A C. Hepatitis, testicular degeneration, and ataxia in DIDO3-deficient mice with altered mRNA processing. Cell Biosci. 2022;12:84.
Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26:139–40.
Author information
Authors and Affiliations
Corresponding author
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Supplementary Information
Additional file 4.
List of genes over- or underexpressed in E16 vs. WT livers.
Additional file 7.
Analysis of compositional biases around splice sites in E16 vs. WT livers.
Rights and permissions
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
About this article
Cite this article
Gutiérrez, J., van Wely, K.H.M. & Martínez-A, C. Correction to: Hepatitis, testicular degeneration, and ataxia in DIDO3-deficient mice with altered mRNA processing. Cell Biosci 12, 144 (2022). https://doi.org/10.1186/s13578-022-00843-1
Accepted:
Published:
DOI: https://doi.org/10.1186/s13578-022-00843-1