Caution
This repo is now outdated. See https://github.com/carpenter-singh-lab/2024_Chandrasekaran_NatureMethods for the profiles used in https://doi.org/10.1038/s41592-024-02241-6.
Infection efficiency interpretation from GPP in CPJUMP1:
-
We see 90-100% typically at 48h but that’s not sufficient time for selection so it’s a bit unreliable - all the cells are still growing pretty happily whether they are infected or not because the Blast hasn't had time to kill them
-
they see 70% for 96h and that is more reliable
Infection efficiency values - CPJUMP-1_I.E_Analysis .xlsx
Level 3, 4a and 4b profiles are in the folder profiles/2020_11_04_CPJUMP1. There are 51 plates
in total and the following are their descriptions
| Barcode | Description | Virus plate name |
|---|---|---|
| BR00117006 | A549 96-hour ORF Plate 2 | DOG.30.31.32.33.A |
| BR00118049 | A549 96-hour ORF w/ Blasticidin Plate 1 | DOG.30.31.32.33.A |
| BR00118050 | A549 96-hour ORF Plate 1 | DOG.30.31.32.33.A |
| BR00118039 | U2OS 96-hour ORF Plate 1 | DOG.30.31.32.33.A |
| BR00118040 | U2OS 96-hour ORF Plate 2 | DOG.30.31.32.33.A |
| BR00117020 | A549 48-hour ORF Plate 1 | DOG.30.31.32.33.A |
| BR00117021 | A549 48-hour ORF Plate 2 | DOG.30.31.32.33.A |
| BR00117022 | U2OS 48-hour ORF Plate 1 | DOG.30.31.32.33.A |
| BR00117023 | U2OS 48-hour ORF Plate 2 | DOG.30.31.32.33.A |
| Barcode | Description | Virus plate name |
|---|---|---|
| BR00118041 | A549 96-hour CRISPR Plate 1 | DXH.92.93.94.95.A |
| BR00118042 | A549 96-hour CRISPR Plate 2 | DXH.92.93.94.95.A |
| BR00118043 | A549 96-hour CRISPR Plate 3 | DXH.92.93.94.95.A |
| BR00118044 | A549 96-hour CRISPR Plate 4 | DXH.92.93.94.95.A |
| BR00118045 | U2OS 96-hour CRISPR Plate 1 | DXH.92.93.94.95.A |
| BR00118046 | U2OS 96-hour CRISPR Plate 2 | DXH.92.93.94.95.A |
| BR00118047 | U2OS 96-hour CRISPR Plate 3 | DXH.92.93.94.95.A |
| BR00118048 | U2OS 96-hour CRISPR Plate 4 | DXH.92.93.94.95.A |
| BR00117003 | A549 144-hour CRISPR Plate 1 | DXH.92.93.94.95.A |
| BR00117004 | A549 144-hour CRISPR Plate 2 | DXH.92.93.94.95.A |
| BR00117005 | A549 144-hour CRISPR Plate 3 | DXH.92.93.94.95.A |
| BR00117000 | A549 144-hour CRISPR Plate 4 | DXH.92.93.94.95.A |
| BR00117002 | A549 144-hour CRISPR w/ Puromycin Plate 1 | DXH.92.93.94.95.A |
| BR00117001 | A549 144-hour CRISPR w/ Puromycin Plate 2 | DXH.92.93.94.95.A |
| BR00116997 | U2OS 144-hour CRISPR Plate 1 | DXH.92.93.94.95.A |
| BR00116998 | U2OS 144-hour CRISPR Plate 2 | DXH.92.93.94.95.A |
| BR00116999 | U2OS 144-hour CRISPR Plate 3 | DXH.92.93.94.95.A |
| BR00116996 | U2OS 144-hour CRISPR Plate 4 | DXH.92.93.94.95.A |
| Barcode | Description | Compound plate name |
|---|---|---|
| BR00116991 | A549 24-hour Compound Plate 1 | C-7210-01-CMP-013 |
| BR00116992 | A549 24-hour Compound Plate 2 | C-7210-01-CMP-013 |
| BR00116993 | A549 24-hour Compound Plate 3 | C-7210-01-CMP-013 |
| BR00116994 | A549 24-hour Compound Plate 4 | C-7210-01-CMP-013 |
| BR00116995 | U2OS 24-hour Compound Plate 1 | C-7210-01-CMP-013 |
| BR00117024 | U2OS 24-hour Compound Plate 2 | C-7210-01-CMP-013 |
| BR00117025 | U2OS 24-hour Compound Plate 3 | C-7210-01-CMP-013 |
| BR00117026 | U2OS 24-hour Compound Plate 4 | C-7210-01-CMP-013 |
| BR00117017 | A549 48-hour Compound Plate 1 | C-7210-01-CMP-013 |
| BR00117019 | A549 48-hour Compound Plate 2 | C-7210-01-CMP-013 |
| BR00117015 | A549 48-hour Compound Plate 3 | C-7210-01-CMP-013 |
| BR00117016 | A549 48-hour Compound Plate 4 | C-7210-01-CMP-013 |
| BR00117012 | U2OS 48-hour Compound Plate 1 | C-7210-01-CMP-013 |
| BR00117013 | U2OS 48-hour Compound Plate 2 | C-7210-01-CMP-013 |
| BR00117010 | U2OS 48-hour Compound Plate 3 | C-7210-01-CMP-013 |
| BR00117011 | U2OS 48-hour Compound Plate 4 | C-7210-01-CMP-013 |
| BR00117054 | A549 48-hour +20% Seed Density Compound Plate 1 | C-7210-01-CMP-013 |
| BR00117055 | A549 48-hour +20% Seed Density Compound Plate 2 | C-7210-01-CMP-013 |
| BR00117008 | A549 48-hour -20% Seed Density Compound Plate 1 | C-7210-01-CMP-013 |
| BR00117009 | A549 48-hour -20% Seed Density Compound Plate 2 | C-7210-01-CMP-013 |
| BR00117052 | A549 Cas9 48-hour Compound Plate 1 | C-7210-01-CMP-013 |
| BR00117053 | A549 Cas9 48-hour Compound Plate 2 | C-7210-01-CMP-013 |
| BR00117050 | A549 Cas9 48-hour Compound Plate 3 | C-7210-01-CMP-013 |
| BR00117051 | A549 Cas9 48-hour Compound Plate 4 | C-7210-01-CMP-013 |
Plate map information is in metadata/platemaps/2020_11_04_CPJUMP1/platemap while other plate
metadata is in metadata/moa.