Processed data can be found in GEO: GSE235063, GSE235308
These data are split into several files and do not require reprocessing if processed/filtered data are used (Data_processing folder)
RNA: raw data (all barcodes) and processed data (barcodes after filtering)
genes.tsv (contains the list of genes)
barcodes.tsv (contains the list of barcodes)
matrix.mtx (contains the expression values)
Also contains metadata per cell (for processed barcodes, see below)
matrix file can be imported using your favorite scRNA analysis package, for Seurat use ReadMtx(mtx=matrix, cells=barcodes, features=genes)
Example of metadata:
header: Cell_Barcode GEO_ID Lambo_et_al_ID Patient_Sample Library_ID Counts Features Mitochondria_percent Classified_Celltype Seurat_Cluster Malignant Patient_ID Biopsy_Origin Age_Months Disease_free_days Clinical_Blast_Percent Expected_Driving_Aberration Subgroup Color_Subgroup Known_CNVs Treatment_Outcome nCount_RNA nFeature_RNA
per cell: AAACCCAAGCGTCAGA-1 PAULSL_Dx_scRNA AML1 Remission AML1_DX 6928 1965 8.28521939953811 Monocytes 9 Normal PAULSL Marrow 22 2586 NA KMT2A-PALM2.AKAP2 KMT2A #8F3FD5 None Censored 6928 1965
scRNA analysis performed for the paper is heavily reliant on Seurat (https://satijalab.org/seurat/) Standard functions included in this package are not included in this repository and can be found using the well annotated tutorials of the Seurat package
ATAC: filtered barcodes.tsv (contains barcodes after filtering)
filtered fragments.tsv (contains fragments from barcodes after filtering)
filtered metadata.tsv (contains metadata per cell, see below)
peaks.tsv (contains identified peaks using MACS2 based on filtered data)
peak_matrix.mtx (contains insertions within peaks)
unfilteredfragments.tsv (for purposes requiring all the fragments)
Fragments can be converted to arrow files using ArchR using the createArrowFiles function on the fragments, which is compatible with scripts in this repository
Example of metadata:
header: Cell_Barcode GEO_ID Lambo_et_al_ID Patient_Sample Library_ID Total_fragments ReadsInTSS ReadsInPeaks FractionInPeaks Classified_Celltype ArchR_clusters Malignant Linked_scRNA_barcode Linked_scRNA_Sample Linked_scRNA_confidence_score Patient_ID Biopsy_Origin Age_Months Disease_free_days Clinical_Blast_Percent Expected_Driving_Aberration Subgroup Color_Subgroup Known_CNV Treatment_Outcome
per cell: CCTTAATGTCATTGGT-1 PAULSL_Dx_scATAC AML1 Diagnosis AML1_DX 99012 49961 114637 0.578927965416936 B.Cell C7 Malignant CATACTTAGTACCCTA-1 AML1_REM 0.736947701403939 PAULSL Marrow 22 2586 NA KMT2A-PALM2.AKAP2 KMT2A #8F3FD5 None Censored
scATAC analysis performed for the paper is heavily reliant on ArchR (https://www.archrproject.com/) Standard functions included in this package are not included in this repository and can be found using the well annotated tutorials on the ArchR website