Project lead: Paul Miller [paulhmiller@gmail.com, pmiller@bccrc.ca]
Data analyzed on Windows 10 and R v3.2.3.
C57BL/6-W41 mice were crossed with NRG mice, the het progeny intercrossed, and then mice homozygous for NOD^Sirp, Rag1-/-, IL2Rg-/-, and Kit^W41 were selected. For the tranplants done by Paul, no further backcrossing was performed (although 2 backcrossing projects, to NRG and C57Bl/6, were done for future experiments). The former (mixed background / "dirty") mice were also crossed with NRG-3GS mice to generate NRG-W41-3GS mice, which Naoto has used as recipients for leukemic cells. But this current project is for the NRG-W41 mice, transplanted with CB cells. There are also BM transplanted mice but there is only one replicate.
Variables include:
- Strain (NRG versus NRG-W41)
- Irradiated (no irradiation versus 900 cGy NRG versus 150 cGy NRG-W41)
- Sex (both strains)
The cell dose used was either 2 or 4 x 10e4 CD34 per mouse. Some experiments used barcoded cells. Note that the 40K cell dose was actually 38K and is sometimes written so.
Experiment names contain a date in YYMMDD format with a letter suffix. Sometimes only the letter is used. But as I cycled through A-Z for my PhD there are muliple experiments for each letter. Difficult to mix them up, but still important to know. These experiment codes are important to distinguish replicates and also to go back to the raw data.
./figures
- contains plotting R scripts and plots. T
./primary_kinetics_pool
- data for primary transplants. CSV files each contain data from multiple experiments, and have both 40K CB CD34+ data and (pooled) 20K and 40K CB data. My analysis shows that the results for 20K and 40K are similar, so pooling is appropriate. There is also data from a single BM transplant experiment. All of these have both BM and PB data sets.
./LDA_secondary
- data and LDA calculation scripts from secondary transplants.
./NSGvsNRG
- data from the NSG versus NRG experiments performed by Kiran and Paul.
./old_age
- Gaby's data from the old age experiments (which was about more than just the age of mice) ./barcoding
- information on the barcoded samples. Currently a bit of a mess as I am still working on this.
./reports
- text and presentation files for external reporting (meetings, grants, etc).
- Units of PB data are in microlitres
- Paul's preferred PB detection threshold is 0.2/uL for leukocytes and 25/uL for platlets.
- There is data for NRG mice irradiated at 150 Rad. I plan to exlude this data as it's difficult to know where it fits in, but others may wish to include it.