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add more info about UHR cell lines
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malachig committed Nov 16, 2023
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### Obtain RNA-seq test data.
The test data consists of two commercially available RNA samples: [Universal Human Reference (UHR)](/assets/module_1/UHR.pdf) and [Human Brain Reference (HBR)](/assets/module_1/HBR.pdf). The UHR is total RNA isolated from a diverse set of 10 cancer cell lines. The HBR is total RNA isolated from the brains of 23 Caucasians, male and female, of varying age but mostly 60-80 years old.
The test data consists of two commercially available RNA samples: [Universal Human Reference (UHR)](/assets/module_1/UHR.pdf) and [Human Brain Reference (HBR)](/assets/module_1/HBR.pdf). The UHR is total RNA isolated from a diverse set of 10 cancer cell lines (breast, liver, cervix, testis, brain, skin, fatty tissue, histocyte, macrophage, T cell, B cell). The HBR is total RNA isolated from the brains of 23 Caucasians, male and female, of varying age but mostly 60-80 years old.

In addition, a spike-in control was used. Specifically we added an aliquot of the [ERCC ExFold RNA Spike-In Control Mixes](/assets/module_1/ERCC.pdf) to each sample. The spike-in consists of 92 transcripts that are present in known concentrations across a wide abundance range (from very few copies to many copies). This range allows us to test the degree to which the RNA-seq assay (including all laboratory and analysis steps) accurately reflects the relative abundance of transcript species within a sample. There are two 'mixes' of these transcripts to allow an assessment of differential expression output between samples if you put one mix in each of your two comparisons. In our case, Mix1 was added to the UHR sample, and Mix2 was added to the HBR sample. We also have 3 complete experimental replicates for each sample. This allows us to assess the technical variability of our overall process of producing RNA-seq data in the lab.

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