| Priyanka | Gad Frankel | 27 samples | IECs distal colon (3.5cm) | BALB/C | Global proteomes MS3 quant.
====
Sample groups (6 groups):
PB36 1 IECs (1.1, 1.2, 1.3 and 1.4 - 4 mice) - PBS group (mock infected)
====
PB36 2 IECs (2.1, 2.2, 2.4 and 2.5 - 4 mice) - CR WT (Citrobacter rodentium infected)
====
PB48 1 IECs (1.1, 1.2, 1.3, 1.4 and 1.5 - 5 mice)) - PBS group (mock infected)
====
PB48 2 IECs (2.1, 2.2, 2.3, 2.4 and 2.5 - 5 mice)- - CR WT (Citrobacter rodentium infected)
====
PB49 1 IECs (1.1, 1.2, 1.3, 1.4 and 1.5 - 5 mice)) - PBS group (mock infected)
====
PB49 2 IECs (2.2, 2.3, 2.4 and 2.5 - 4 mice)- - CR WT (Citrobacter rodentium infected) |
| Sample pooling scheme:
Per sample group, all mice samples (4 or 5 mice) were pooled in equal amounts (25ug if 4 mice or 20ug if 5 mice) to get six sample 100ug pools and digested with trypsin. Digestion was very good with 97% 0 missed cleavages. 25ug was taken, dried down, resuspended in 25ul TEAB, and labeled using 10ul TMT10plex. Fractionated into 24 fractions, resuspended in 62.5ul for MS analysis (0.1 ug/ul), and injected 10ul.
A premix analysis was run - samples fractioned into 24 final pools of bRP fraction using a 30-second scheme using offline HPLC.
Sample left: Samples can still be used for MS runs (inject 10ul for 1ug peptide per fraction) |