Literature DB >> 36056442

Correction to: Hepatitis, testicular degeneration, and ataxia in DIDO3-deficient mice with altered mRNA processing.

Julio Gutiérrez1, Karel H M van Wely2, Carlos Martínez-A2.   

Abstract

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Year:  2022        PMID: 36056442      PMCID: PMC9440595          DOI: 10.1186/s13578-022-00843-1

Source DB:  PubMed          Journal:  Cell Biosci        ISSN: 2045-3701            Impact factor:   9.584


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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. 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.
  3 in total

1.  StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.

Authors:  Mihaela Pertea; Geo M Pertea; Corina M Antonescu; Tsung-Cheng Chang; Joshua T Mendell; Steven L Salzberg
Journal:  Nat Biotechnol       Date:  2015-02-18       Impact factor: 54.908

2.  Hepatitis, testicular degeneration, and ataxia in DIDO3-deficient mice with altered mRNA processing.

Authors:  Julio Gutiérrez; Karel H M van Wely; Carlos Martínez-A
Journal:  Cell Biosci       Date:  2022-06-07       Impact factor: 9.584

3.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937

  3 in total

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