Aggregate of ~900k Human Non Small Cell Lung Cancer and Normal Adjacent Cells, Multiplexed Samples, 16 Probe Barcodes (Next GEM)

This dataset is part of the Scaling comparative lung cancer studies using Chromium Single Cell Gene Expression Flex Application Note.

32 flash frozen tissues from two major subtypes of treated and untreated Non Small Cell Lung Cancer (NSCLC) (Lung Adenocarcinoma and Lung Squamous Cell Carcinoma) and Normal Adjacent samples were obtained by 10x Genomics from BioIVT ASTERAND.

Sample size	Probe Barcode per sample

(Left) Sample sizes by tumor subtype and clinical stage. The NSCLC tumor subtypes are displayed by row: Lung Adenocarcinoma (LUAD); Treated Lung Adenocarcinoma (LUAD_Tx); Normal Adjacent (NADJ); Lung Squamous Cell Carcinoma (LUSC); and Treated Lung Squamous Cell Carcinoma (LUSC_Tx). Clinical stages are displayed by column.

(Right) 32 samples were split into two unique 16-plex pools and labeled as Samples 1-16 and Samples 17-32. The two right hand columns list the samples within each 16-plex pool, notated by tumor subtype and clinical stage. The left column lists the Probe Barcode associated with a particular sample.

Tumor tissues were fixed for 20 hours at 4°C following the demonstrated protocol Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling (CG000553).

The Fixed RNA Gene Expression library was generated as described in the Chromium Fixed RNA Profiling for Multiplexed Samples User Guide (CG000527). Samples were run as a 16-sample multiplexed experiment, in which each sample was hybridized with a unique Probe Barcode in a separate hybridization reaction. After hybridization, samples were pooled in equal proportions, washed, and then run in replicates across four GEM lanes each. The resulting libraries were sequenced on an Illumina NovaSeq6000 with approximately 20k read pairs per cell.

• Total 897,733 cells detected

  • NADJ: 254,429
  • LUAD: 168,978
  • LUAD_Tx: 123,642
  • LUSC: 225,536
  • LUSC_Tx: 125,148

• Paired-end, dual indexing: 28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2

The sample-level web summaries from the cellranger multi runs are available for download here.

Note: This dataset has Low Post-Normalization Read Depth due to a large discrepancy in the sequencing depth per cell between samples in the library.

This Single Cell Gene Expression Flex (Multiplex) data set is derived from commercially purchased, fully de-identified biospecimens (for research use only) obtained from BioIVT, LLC (formally Asterand Bioscience) and collected in accordance with their Certificate of Compliance in accordance with U.S. and international law and consents. The resulting data from the biospecimens are provided for free to the research community to use and analyze without limitation, including for grants, publication and development purposes. However, because the data set is made available to the public at no charge, and 10x Genomics has no control over how you choose to use it, 10x Genomics, Inc. cannot be responsible for and expressly disclaims any and all liability due to your use, publication or reliance on the data.

Loupe demo tutorial dataset

A subset (n=21) of 32 flash frozen tissues from treated and untreated Non-Small Cell Lung Cancer (Lung Squamous Cell Carcinoma, LUSC) and Normal Adjacent (NADJ) samples were obtained by 10x Genomics from BioIVT ASTERAND.

For this specific analysis, LUAD samples were excluded. Tumor tissue samples were fixed for 20 hours at 4°C following the demonstrated protocol Tissue Fixation & Dissociation for Chromium Fixed RNA Profiling (CG000553). The Fixed RNA Gene Expression library was generated as described in the Chromium Fixed RNA Profiling for Multiplexed Samples User Guide (CG000527). Samples were run as a 16-sample multiplexed experiment, in which each sample was hybridized with a unique Probe Barcode in a separate hybridization reaction. After hybridization, samples were pooled in equal proportions, washed, and then run in replicates across four GEM lanes each.

The resulting libraries were sequenced on an Illumina NovaSeq6000 with approximately 20k read pairs per cell.

• Total 157,323 cells detected (NADJ: 65,709; LUSC: 58,593; LUSC_Tx: 33,021)
• Paired-end, dual indexing: 28 cycles Read 1, 10 cycles i7, 10 cycles i5, 90 cycles Read 2

Note: this dataset has Low Post-Normalization Read Depth due to a large discrepancy in the sequencing depth per cell between samples in the library.

This Single Cell Gene Expression Flex (Multiplex) data set is derived from commercially purchased, fully de-identified biospecimens (for research use only) obtained from BioIVT, LLC (formally Asterand Bioscience) and collected in accordance with their Certificate of Compliance in accordance with U.S. and international law and consents. The resulting data from the biospecimens are provided for free to the research community to use and analyze without limitation, including for grants, publication, and development purposes. However, because the data set is made available to the public at no charge, and 10x Genomics has no control over how you choose to use it, 10x Genomics, Inc. cannot be responsible for and expressly disclaims any and all liability due to your use, publication or reliance on the data.

This dataset is licensed under the Creative Commons Attribution license.