Skip to content
This repository has been archived by the owner on Nov 14, 2024. It is now read-only.

Latest commit

 

History

History
89 lines (74 loc) · 5.7 KB

README.md

File metadata and controls

89 lines (74 loc) · 5.7 KB
Raw

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This repo is now outdated.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.

CPJUMP1 profiles

Other data

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

JUMP Cell Painting CPJUMP1 Pilot profiles metadata

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

All the ORF plates

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

All the CRISPR plates

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

All the compound plates

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.