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Supporting Data

Raw total RNA-Seq data were deposited on the SRA database through GSE52405 accession number.

lncRNA_NONCODEv3_Guttman2011.fa - fasta file of LncRNA sequences. Sequences were retrieved from NONCODEv3. 209 additional sequences from Gutman et al. were retrieved from Table S1 and manually curated before addition to our database (11 duplicated lncRNAs from Guttman 2011 were removed and sequences that were identical to lncRNA from NONCODEv3 were also filtered out).

Annotations_NonCodingGenes_over_GRCm38.gtf - GTF file of lncRNA transcripts in MONOCLdb ; M. musculus GRCm38.70 (MM10).

Gene_Counts_Scaled.txt - tab separated file of scaled normalized gene counts for 40,566 genes, including 19,838 coding and 20,728 non-coding genes, quantified with at least one read count across the experiment.

Genes_Annotations.txt - tab separated file. Mapping between MONOCLdb lncRNA gene ID and NONCODE v3.0 lncRNA transcript ID. Transcripts with overlapping exons (> 50% sequence overlap) were aggregated at the gene level . The column DESCRIPTION was derived from NONCODE v3.0, which provides the "accn","class","Source" for each lncRNA. These field were concatenated at the gene level with "//" separating annotation for each transcript. For coding genes, annotation was downloaded from Ensembl release 70.

Expression_Heatmap.txt - tab separated file of mean log2 fold change (FC) value for each infected condition, defined as the arithmetic average of individual log2 FC = log2(sample x) - mean (log2(mice strain-matched mocks)). The column QC indicates whether gene raw counts >= 10 in more than 75% of the samples of at least 1 biological condition (QC = 1), or not (QC = 0).PADJ column is the adjusted p-value assessed using the negative binomial model implemented in DESeq which was used to test differential expression between infected samples and mocks.

Module-based_Enrichment.txt - tab separated file indicating module membership for each lncRNA (column "MODULE") and percentile ranks for intramodular degree (column "HUB") and for betweeness centrality (column "BN").

Rank-based_Enrichment.txt - tab separated file indicating module membership for each lncRNA (column "MODULE") and percentile ranks for intramodular degree (column "HUB") and for betweeness centrality (column "BN").

Co-Expression_Network.txt - tab separated file of top 15 most correlated DE genes (|bicor| > 0.7 listed in parentheses) with each lncRNA.

Genomic_Network.txt - tab separated file compiling data used to generate the genomic network. The list of DE genes strongly correlated with each lncRNA (|bicor| > 0.7) is reported in the column "GENES_BICOR_SUP07". Columns "MIDDLE" and "CHR" describes chromosomic coordinates. Columns "ISCIS" and "ISTRANS" indicate whether lncRNA was classified as potential cis or trans regulator, respectively.

Pathogenicity_Association.txt tab separated file of bicor coefficient measuring correlation between gene expression profiles and : weight loss (WL), viral genomic RNA (vRNA) or viral mRNA (vmRNA).

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