# Acquisition Decision: idr0071 Experiment C

## Study structure

- Project ID 1504 on IDR (project, not screen)
- 6 wells: A1, A2, A3, B1, B2, B3
- 533 tiles per well (3,198 total)
- Per-tile processed outputs: reads.csv, bases.csv, cells.tif, nuclei.tif, phenotype_aligned.tif, aligned.tif, log.tif
- cells.csv and phenotype.csv NOT on FTP — must be derived from reads.csv

## Barcode-to-gene mapping

- CROPseq_NFkB_library.csv: 5,738 sgRNAs targeting 949 real genes + 100 non-targeting controls
- reads.csv barcodes are 9-mer SBS base calls
- Mapping uses sgRNA[:9] prefix match (no collisions, all 5,738 unique)
- Per tile: ~138 cells called, ~56 unique genes detected

## Size estimates

| Data type | Per tile | All 3,198 tiles | Budget fits? |
|-----------|----------|-----------------|--------------|
| reads.csv | ~2 MB | ~6.2 GB | NO |
| phenotype_aligned.tif | ~4 MB | ~12.5 GB | NO |
| cells.tif | ~2 MB | ~6.2 GB | NO |

## Decision: Two-well minimal path

Download reads.csv for wells **A1** and **B1** only (1,066 tiles).

- Estimated size: ~2.1 GB (within 5 GB cap)
- Expected yield: ~147K cells, ~800+ genes
- Sufficient for gene-disjoint vs. random split comparison
- Two independent biological replicates provide reproducibility check

## Files to download

1. CROPseq_NFkB_library.csv (277 KB) — DONE
2. well_tile_list.csv (22 KB) — DONE
3. reads.csv for A1 tiles: 533 files (~1.05 GB)
4. reads.csv for B1 tiles: 533 files (~1.05 GB)
5. phenotype_aligned.tif for A1 tiles: 533 files (~2.1 GB) — ONLY IF time/space allows after reads