Meeting Minutes

September 8, 2017

Current status of HRDP

1. Small RNA still needs one/two batches (59 samples) to complete 3 biological replicates across liver/brain
2. Total RNA done for 43 strains / 3 biological replicates - need to add the redo samples

To be done soon to complete data for 43 strains:

• incorporate redos
• missing smRNA batches (waiting on PO)
• COP DNA-Seq

To be done to complete database:

• inbred reconstructions (Harry)
• HRDP methods for eQTL, heritability, co-expression (Lauren)
• algorithm for identifying protein-coding capacity

Unique characteristics of our total RNA database

• strandedness
• isoforms
• liver/brain
• non-coding
• heritability
• genetic correlations

Possible paper focus

1. Protein-coding vs non-coding - heritability; connectivity; substrains
2. Genetic vs. tissue driven diff - expression; characteristics; co-expression; substrain

September 1, 2017

The goal of this meeting was to discuss the status of the HRDP sequencing.

RNA extraction and library preparation

Jenny's has a database to keep track of each sample. It is stored on Tabastore3. She needs to update it for the latest batch and will notify Spencer and Lauren when done.

Sequencing

1. Liver total and small is done for 3 biological replicates of the RIs and the Inbreds
2. Brain total and small is done for 3 biological replicates of the inbreds and 1-2 biological replicates of the RIs
3. Recent received a batch that has redos of many samples. It still needs to be downloaded and processed

Processing

• All total RNA libraries generated have been processed to the point of RSEM counts for the Ensembl transcriptome and the transcriptome reconstructed from the BNLx and SHR strains using strain-specific transcriptomes (SNP only)
• The only exception is the recently received batch of redos (both brain and liver)
• Small RNA were recently quantitated

Analyzing

• All total RNA libraries have been normalized and are available on PhenoGen (need to double check) with the exception of the recently received batch of redos
• Lauren will work on the normalization of the small RNA quantitation

Next in the pipeline

• Jenny has ordered tissues from the parental strains of the FEXL/LXFE panel from Japan

Long term goals

• formal QC report per library
• HRDP analysis tools evaluated for co-expression and eQTL
• Transcriptome reconstruction in inbreds
• evaluation of spike-ins

TO-DOs

Jenny - update prep database and send to Spencer/Lauren/Laura

Lauren - gather sample information to follow individual samples from RNA extraction in final expression data set (extracted, prepped, sequenced, processed, on PhenoGen); normalize small RNA quantitation

Spencer - continue to update master database to make accessible to all staff