SampleSheet.py

SampleSheet.py generates Illumina Sample Sheets that encode barcode-to-sample relationships for demultiplexing and downstream genotypic and regulatory-motif analyses of CRISPR-Cas9–edited cell populations.

Key Features:

• Automation of Sample Sheet Creation: SampleSheet.py automates construction of Illumina Sample Sheets encoding up to 9,216 unique barcode-sample relationships.
• Illumina barcode compatibility: Leverages a panel of 192 8-nucleotide i7 and i5 barcode primers compatible with Illumina sequencing platforms.
• Integration with analytical scripts: Integrates with ImputedGenotypes.py and CollatedMotifs.py to define alleles, impute genotypes from demultiplexed fastq files, and identify altered regulatory factor binding motifs.
• Facilitation of genetic diversity evaluation: Enables large-scale assessment of allelic diversity across many samples through combinatorial barcoding and downstream genotype imputation.

Scientific Applications:

• Cas9-Edited Cell Population Analysis: Supports surveying allelic diversity generated by Cas9-targeted DNA cleavage and repair in edited cell populations.
• Regulatory Motif Identification: Assists identification of altered transcription factor recognition motifs resulting from genetic edits when used with CollatedMotifs.py.
• FKBP5 glucocorticoid receptor site studies: Has been applied to studies targeting glucocorticoid receptor binding sites near FKBP5 in human adenocarcinoma cell lines.

Methodology:

Employs permutations of i7 and i5 barcodes (192 8-nucleotide primers) to uniquely label samples, automates Illumina Sample Sheet generation, and—together with ImputedGenotypes.py and CollatedMotifs.py—performs genotype imputation from demultiplexed fastq files and detection of altered regulatory motifs.