Additional file 9 of Identification of long noncoding RNAs in injury-resilient and injury-susceptible mouse retinal ganglion cells
Creators: name: Ayupe, Ana C.
name: Beckedorff, Felipe
name: Levay, Konstantin
name: Yon, Benito
name: Salgueiro, Yadira
name: Shiekhattar, Ramin
name: Park, Kevin K.
Publisher: name: figshare
Year: 2021
Subjects: subject: Genetics
subject: FOS: Biological sciences

description: Additional file 9: Fig. S1 Subclasses of lncRNAs detected in ipRGCs and ooDSGCs. Venn diagram showing antisense lncRNAs (AS lncRNAs) (a), long intergenic noncoding RNAs (lincRNAs) [b] and novel lincRNAs (c) expressed under normal and injury (i.e. optic nerve crush) conditions. Fig. S2 RGC type specificity of lncRNAs and protein-coding genes using a fractional expression level (FEL) across normal and injured ipRGCs and ooDSGCs. Relative abundance of the lncRNAs (n = 1415) (a) and mRNAs (n = 13,366) (b) expressed in at least one of the four RGC groups. For each sample, transcript abundance is expressed as a fraction of the sum of the expression values detected in all RGC types (FEL) (see Methods for details). (c) Maximal expression abundance (log2-TPM) of each lncRNA and protein-coding across the four RGC groups. The right panel shows the expression levels of 478 lncRNAs (top right) and 3735 protein-coding genes (bottom right) that have a maximal expression level within the range bounded by the dashed segments in the left panel ([2–4.32] log2 TPM). (d) FELs of lncRNAs and mRNAs expressed at the full TPM expression range and with maximal expression level within the range 4–20 TPM across the four RGC groups were calculated. The percentages of transcripts with an FEL higher or lower than 50% in each class are shown. Higher FEL values indicate higher specificity for RGC types. The observed fractions of RGC type specific lncRNAs are significantly different compared to those of the mRNAs at the full TPM range and at the 4–20 TPM range. (***) Chi-square test, p |0.5| (vertical red dashed lines) were considered as correlated. The square of the correlation coefficient (r2) in the regression linear between Y and X-axis is shown in each panel. Fig. S6 Heat map showing the expression level of mRNAs that are correlated neighbors (r &gt; |0.5|) of the differentially expressed lncRNAs. (a) Injured ooDSGCs vs. normal ooDSGCs. (b) Injured ooDSGCs vs. injured ipRGCs. (c) Normal ooDSGCs vs. normal ipRGCs. Expression values were based on Z-score normalized TPM for each mRNA. Fig. S7 Heat map displaying the correlation between the lncRNAs and a subset of mRNAs from the cluster 2 from Fig. 5a that were enriched in the Biological Processes terms “intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress” (a) and “positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress” (b). LncRNAs in purple and green fonts are upregulated and downregulated, respectively, in the injured ooDSGCs vs. normal ooDSGCs comparison. Red to blue Pearson Correlation scale indicates the degree to which mRNA expression is positively (dark red), negatively (dark blue), or not correlated with the expression of the respective lncRNA.