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HIV-1 Tat and Cocaine Coexposure Impacts PIWI-Interacting RNAs (piRNAs) to Affect Astrocyte Energy Metabolism. Supplementary figures and tables

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posted on 2022-02-16, 10:36 authored by Mayur Doke, Fatah Kashanchi, Mansoor A. Khan, Thangavel Samikkannu

Supplementary Figure 1

A) Table listing the 27 common piRNAs. B) Venn diagram of the DE piRNAs identified in the group comparisons and the 27 piRNAs that were shared among all three comparisons: control vs. HIV-1 Tat, control vs. cocaine and control vs. HIV-1 + cocaine (TC). C) Table listing the 42 common piRNA-targeted genes. D) Venn diagram of the DE piRNA-targeted genes identified in the group comparisons and the 42 piRNA-targeted genes that were shared among all three comparisons: control vs. HIV-1 Tat, control vs. cocaine and control vs. TC.

Supplementary Figure 2

Functional analysis of piRNA-targeted genes. A) GO analysis of the 102 piRNA-targeted genes was performed using Cluster Profiler GO. The top 15 significantly (P ≤ 0.05) enriched GO terms are shown. B) Molecular function identification was carried out with the PANTHER classification system, and GO terms were retrieved. The top 15 significantly (P ≤ 0.05) enriched GO terms in the molecular function category are shown.

Supplementary Figure 3

A) The involvement of the piRNA-targeted genes in various pathways was investigated using KEGG pathway analysis. A list of the most enriched KEGG pathways in which genes were involved is shown. B) Involvement of the genes in various component/metabolic pathways. C) GO analysis of the 102 common piRNA-targeted genes was performed using Cluster Profiler GO, and the involvement of 71 genes in various KEGG pathways was evaluated. The four target genes that were differentially enriched are shown in red colored highlighted boxes- ADH4- K13951 alcohol dehydrogenase 1/7 [EC:1.1.1.1], NUDT9 - K13988 ADP-ribose pyrophosphatase [EC:3.6.1.13], UGDH- K00012 UDPglucose 6-dehydrogenase [EC:1.1.1.22], ENTPD1- K01510 apyrase [EC:3.6.1.5] and RDH16- K11154 retinol dehydrogenase 16 [EC:1.1.1.-]

Supplementary Table 1- Concentration measurement and quality assessment of small RNA for all samples.

Supplementary Table 2- Number of raw reads in our small RNA-seq libraries.

Supplementary Table 3- piRNA clusters with their chromosomal locations and transcript per million (TPM) values.

Supplementary Table 4- Percentage of mapping of cleaned reads to the human genome for our small RNA-seq libraries.