Information for qiagen ipa class

We are using the datasets below in the Qiagen IPA course.

Human Brain Reference (HBR) and Univeral Human Reference (UHR) dataset

  • Using this for the one hour lecture (from 1 - 2 pm)
  • Find more information about the HBR and UHR dataset at RNA Bio, but essentially this is a RNA sequencing study, where
    • UHR RNA samples were derived from a diverse set of 10 cancer cell lines
    • HBR RNA samples were isolated from brains of 23 Caucasians - male and females, with varying ages.
  • Data was subsetted to those sequencing reads that map to human chromosome 22 (so this is a small dataset)
  • Differential expression analysis results in hbr_uhr_deg_chr22.csv
    • foldChange column is actually the ratio between mean expression in UHR sample and mean expression in HBR sample (ie. UHR mean expression/HBR mean expression)

HCC1395 dataset

  • Using this for the one hour practice session after the lecture (from 2 - 3 pm)
  • Find more information about this dataset at RNA Bio, but essentially this is a tumor versus normal transcriptome comparison where RNA was extracted from
    • HCC1395 breast cancer cell line (tumor)
    • HCC1395BL matched lymphoblastoid cell line (normal)
  • Data was subsetted to those sequencing reads that map to human chromosome 22 (so this is a small dataset)
  • Differential expression analysis results in hcc1395_deg_chr22.csv
    • foldChange column is actually the ratio between mean expression in tumor and mean expression in normal (ie. tumor mean expression/normal mean expression)