morrislab/pcg-ess

Overview:

This dataset measures the essentiality of protein-coding genes (PCGs) as measured by Liang et al. 2024. In a pooled CRISPR screen, 10 guide RNAs (gRNAs) were designed per specific PCG transcript to knock them down. The log-fold change of these gRNAs were measured at 7 days (not included in this data) and 14 days. This experiment was repeated across several cell lines. Transcripts are further classified as non-essential if it is not expressed in a cell line, or if knockdown did not result in a large log-fold change at 14 days. See paper for exact procedure used to determine essentiality classification.

This dataset was synthesized using Table S1 and Table S2 from the original paper.

Data Format

Description of data columns:

• target_log2fc_{cell-line}: Log-fold change in expression of guide RNA targeting specific PCG trancsript at day 14 for specific cell line.
• target_essential_{cell-line}: Essentiality of transcript. Transcripts are considered non-essential if it is not expressed in the cell line or knockdown does not have major effect on gRNA expression.
• cds: Binary track which reports position of first nucleotide in each codon in CDS.
• splice: Binary track which reports position of the 3' end of each exon, indicating splice sites.

Data Source:

Data was collected from Table S1 and Table S2 of "Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells" and is redistributed with the author's permission. Please provide proper attribution if you use this dataset, and contact the author for permission regarding further redistribution.

Original paper: https://www.cell.com/cell/fulltext/S0092-8674(24)01203-0
Original data sources:

• https://www.cell.com/cms/10.1016/j.cell.2024.10.021/attachment/e8206fae-f07b-4102-a5b9-f07beb7d20da/mmc1.xlsx
• https://www.cell.com/cms/10.1016/j.cell.2024.10.021/attachment/8b158086-74ff-4b8d-b3cc-d32917f6908d/mmc2.xlsx

Citation: Liang, Wen-Wei, et al. "Transcriptome-scale RNA-targeting CRISPR screens reveal essential lncRNAs in human cells." Cell 187.26 (2024): 7637-7654.