Supplementary Materials

The PDF file includes:

  • Materials and methods
  • Fig. S1. Flow cytometry gating strategies and quality control of HIV-1 SortSeq.
  • Fig. S2. HIV-1 SortSeq+ cells from HIV-1–infected individuals harbor spliced HIV-1 RNA.
  • Fig. S3. HIV-1 SortSeq can identify clonally expanded HIV-1–infected cells harboring replication competent HIV-1.
  • Fig. S4. Transcriptional profile of housekeeping genes B2M and UBC in HIV-1 SortSeq+ and SortSeq single cells.
  • Fig. S5. Gene ontology analysis of differentially expressed genes in HIV-1 SortSeq+ versus SortSeq cells from ART-treated, virally suppressed, HIV-1–infected individuals.
  • Fig. S6. Expression levels of IMPDH1, JAK1, UPF2, and IKBKB in HIV-1 SortSeq+ and SortSeq single cells measured by qPCR.
  • Fig. S7. HIV-1–host chimeric RNA landscape.
  • Fig. S8. Orientation and integration sites of induced HIV-1 proviruses in HIV-1 SortSeq+ cells.
  • Table S1. Characteristics of study participants.
  • Table S2. Genes in which HIV-1 is integrated.
  • Table S3. HIV-1–host RNA junctions.
  • References (7687)

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Other Supplementary Material for this manuscript includes the following:

  • Data file S1 (Microsoft Excel format). Primary data.
  • Data file S2 (Microsoft Excel format). HIV-1 SortSeq probe sequences.
  • Data file S3 (.docx format). Location of HIV-1 SortSeq probes.
  • Data file S4 (Microsoft Excel format). List of HIV-1 SortSeq samples.
  • Data file S5 (Microsoft Excel format). Differentially expressed genes between HIV-1 Sortseq+ and Sortseq cells.