Full chip, mixture of drug treated H1975 and A549 cells, targeted gene expression (gene signature)

Human A549 and human H1975 cell lines were seeded in biological replicates on two 96 well plates. Cells were either untreated, or treated with various drugs (erlotinib, crizotinib, osimertinib, linsitinib, or combinations) for 4, 16, or 24 hours in technical replicates. Each treatment condition was CellPlexed. Technical replicates of both cell lines across each time point were pooled for each drug/drug combination.

Gene expression and CellPlex libraries were generated as described in the Chromium Next GEM Single Cell 3' HT Reagent Kits v3.1 User Guide with Feature Barcode technology for Cell Multiplexing (CG000419 Rev A).

Libraries were combined into two pools of 8 libraries. Targeted gene expression libraries were generated as described in the Targeted Gene Expression - Single Cell User Guide (CG000293 Rev E) using the Human Gene Signature Panel (1,142 genes, PN-1000245) and sequenced on Illumina NovaSeq 6000 to a depth of approximately 6,000 raw reads per cell.

28 cycles Read 1 (16bp barcode, 12bp UMI), 10 cycles i7 (index), 10 cycles i5 (index), 90 cycles Read 2 (transcript).

Data were analyzed as follows:

1. Targeting and CellPlex libraries for each GEM well were analyzed with cellranger multi; --expect-cells=60000; GEX reference: GRCh38-2020A; target panel: see input link below.
2. The results were combined using cellranger aggr.

FASTQ files: Due to the large size of the data, the raw FASTQ data will not be available directly from our website. Users can pay to download the raw FASTQ data from Amazon S3 at their cost. The instructions to download the FASTQs are here.

Note: this dataset has Low Post-Normalization Read Depth because there is a large discrepancy in sequencing depth among the input libraries.

This dataset is licensed under the Creative Commons Attribution license.