Experimental Data

Download link here
Excel file including raw un-normalized
  1. mRNA data: twelve HIV, and twelve mock samples (SAGE-seq data).
  2. miRNA data: twelve HIV, and twelve mock samples (ShortRNA-seq data).
  3. HIV integrations: List of identified loci with proviral integration in them at hour 24 post infection.
  4. Viral Measurements: Measurements of nine viral intermediates in the HIV infected samples over the twelve time points(RT-qPCR, FACS, ELISA depending on the marker).
  5. mRNA data from validation samples: six HIV, six mock samples , as well as six samples "infected" with heat-inactivated virus, and six samples infected with [90%+10%] heat-inactivated virus and normal virus (SAGE-seq data).

HIV collection

Download link: here A compilation list of HIV related gene sets in the GMT format in which, each row corresponds to one geneses (File: HIV_Collection.gmt.txt). For details on the .gmt format see: 3.2 GMT: Gene Matrix Transposed file format (*.gmt)
The rest of the gene collections used in this work, are available on their original sources: Peachi website.