Exam 1- Lecture 8 Flashcards
What is the workflow of RNA-seq
Total RNA —>
mRNA enrichment
or
rRNA depletion—-> RNA fragmentation—–>
ds cDNA—-> DNA workflow
Explain RNA fragmentation
chemical shear for long RNA fragments
heat digestion of RNA with a divalent metal cation
What does RIN stand for
RNA integrity number
What does RIN do
algorithm for assigning integrity values to RNA measurements
Why is RIN important
integrity of RNA is major concern for gene expression studies
What is DV200
percentage of RNA fragments that are >200 nucleotides in size
What is the function of SMART-Seq v4 Ultra Low Input RNA
generate high quality full length cDNA directly from multiple cells or RNA
What is the function of Zymo-seq
make stranded, rRNA free total RNA libraries
What does Zymo-seq use
an enzyme that binds RNA/DNA duplexes and degrade DNA
What is BioCyc
collection of Pathway/Genome Databases that provide reference to genome and metabolic pathway information
What happens during droplet based single cell RNAseq
starts with gel bead and cell
cell lysis and gel bead dissolution
Read 1- Cell ID and UMI
Read 2- Gene 3’ sequence
What happens during plate based single cell RNAseq
microwell cell loading
cell lysis and reverse transcription
cDNA fragmentation
cell specific barcode ligation
Both reads- Cell ID
Gene sequence
