RID Data Submission

Users are welcome to submit integration site information and patient demographics in the following Excel templates (examples are shown in these templates):

1. Integration site data (download the template here)
hosthost genome buildvirusvirus subtypepatient/sample_idtissuesite_id_used_in_paperchromosomepositionprovirus_strandLTRcountcommentpubmed_id
Homo sapienshg19HIV_1BC906PBMCc906_1chr1160471168-5LTR112345678
C906PBMCc906_2chr1076173663-both5
A907CD4+NAchr1173418996+5LTR1
ATL8PBMCATL8-1chr12122963485-5LTR3
ATL9PBMCATL9-3chr1320262176+both1
ATL10PBMCNAchr1569965142+3LTR1

  • Host, host genome build, virus, subtype, and PubMed ID only need to be entered once in the data submission Excel file.
  • Provirus strand is defined as “+” if the provirus integrated in the same orientation as the chromosome being integrated and “-“ if the provirus integrated in the opposite orientation.
  • If information is not available, “unknown” should be entered in the column. However, host, host genome build, virus, subtype, sample/patient, tissue, chromosome, position, provirus_strand, and LTR are necessary for data submission.
2. Patient demographic if available (download the template here)
patient_idtissueage(yr)genderrace/eithnicitytrasmission_moderetrovirus_diagnosis_date(MM/DD/YYYY)plasma_viral_RNA_level_at_diagnosisCD4_nadirdisease_classificationtherapytherapy_initiation_date(MM/DD/YYYY)therapy_duration(yr)sampling_dateclinical_status_and_comorbid_illness_at_samplinginfection_duration_prior_to_sampling(yr)disease_classification_duration_prior_to_sampling(yr)therapy_duration_prior_to_sampling(yr)proviral_DNA_copies_at_samplingviral_RNA_copies_at_diagnosisviral_RNA_copies_at_samplingabsolute_lymphocite_count(10^9/L)CD4_at_diagnosisCD4_at_samplingCD4_before_therapynumber_clones_detectedoligconality_index(Gini_index)sample_comment
C906PBMC59FBlackMSN8/8/00TDF+FTC+RTG8/9/00178/8/1750 copies/1 million PBMC5.4 log10/copies ml plasma2.1 log10 copies/ml plasma22 cells/µl
A907PBMC6MBlackmother to child8/8/12TDF+FTC+NVP8/9/1258/9/1751 copies/1 million PBMC3.9 log10/copies ml plasma< 1.7 log10 copies/ml plasma243 cells/µl
B909CD459FWhitedrug use8/8/05TDF+FTC+ATZ/r8/10/05128/10/1752 copies/1 million PBMC5.6 log10/copies ml plasma2.9 log10 copies/ml plasma24 cells/µl
ATL8PBMC69FWhite1/1/07ATL8/11/08diagnosis83 copies/100 PBMC43.92.43%
ATL9PBMC55MCaribbean2/1/05ATL8/12/08complete remission83 copies/100 PBMC43.92.43%
ATL10PBMC70MBlack6/7/99ATL8/13/08relapse83 copies/100 PBMC43.92.43%

The integration site data and patient demographics should be sent via email to Wei Shao at rid@mail.nih.gov with the Excel file(s) attached.