Dataset DOI: 10.5061/dryad.s7h44j1ph

Description of the data and file structure

This dataset contains single‑cell RNA sequencing (scRNA‑seq) data from two head and neck squamous cell carcinoma (HNSCC) patient‑derived xenograft (PDX) models, UW‑SCC‑185 (cetuximab‑sensitive) and UW‑SCC‑194 (cetuximab‑resistant), treated with vehicle or cetuximab. This goal of this dataset is to compare treatment-sensitive and treatment-resistant tumors and test the hypothesis that low AXL correlates with clinical response to cetuximab in patients with head and neck cancer (HNC). 

Biological replicates (n = 10 for UW-SCC 185, n = 12 for UW-SCC 194) were combined prior to dissociation to encompass biologic heterogeneity. Dissociation from solid tumor to single cell suspension was performed as described previously in Berube et al., 2024, protocols.io. High quality cell suspensions were prepared with an average viability of over 75%. scRNA-seq libraries were constructed using the PIPseq 3’ Single Cell RNA Kit v4.0Plus (T20 for UW-SCC 185, T2 for UW-SCC 194), following the manufacturer’s protocol. For UW-SCC 185 one T20 vial was used for each treatment group and for UW-SCC 194 two T2 vials were used for each treatment group to increase total number of cells sequenced. Libraries were sequenced on an Illumina NovaSeq X sequencer with a sequencing depth of at least 20,000 reads per cell. Each .zip folder described below contains raw FASTQ files.

Files and variables

The FASTQ naming structure is not identical across all files. Naming conventions differ between runs because each patient‑derived xenograft (PDX) model was processed and sequenced separately.

File: UW-SCC194_ctrl.zip

Description: Contains 4 individual FASTQ files

• 30067_1_R1_001.fastq.gz
• 30067_1_R2_001.fastq.gz
• 30067_2_R1_001.fastq.gz
• 30067_2_R2_001.fastq.gz

Using the naming strategy a_b_c_d.fastq.gz	

	a) sample number used internally for sample identification; this sample is from the control group

	b) index of PIPseq vials: 1 for the 1st vial and 2 for the second vial

	c) read number (either R1 or R2 for paired-end reads)

	d) final segment, which is always 001

File: UW-SCC194_ctx.zip

Description: contains 4 individual fastq files

• 30068_1_R1_001.fastq.gz
• 30068_1_R2_001.fastq.gz
• 30068_2_R1_001.fastq.gz
• 30068_2_R2_001.fastq.gz

Using the naming strategy a_b_c_d.fastq.gz	

	a) sample number used internally for sample identification; this sample is from the cetuximab-treated group

	b) index of PIPseq vials, 1 for the 1st vial and 2 for the second vial

	c) read number (either R1 or R2 for paired-end reads)

	d) final segment, which is always 001

File: UW-SCC185_ctrl_S1.zip

Description: Contains 6 individual fastq files

• 2023-12-11-pip-ctrl_S1_L001_R1_001.fastq.gz
• 2023-12-11-pip-ctrl_S1_L001_R2_001.fastq.gz
• 2023-12-11-pip-ctrl_S1_L002_R1_001.fastq.gz
• 2023-12-11-pip-ctrl_S1_L002_R2_001.fastq.gz
• 2023-12-11-pip-ctrl_S1_L003_R1_001.fastq.gz
• 2023-12-11-pip-ctrl_S1_L003_R2_001.fastq.gz

Using the naming strategy a-b-c_d_e_f_g.fastq.gz	

	a) sample submission date

	b) library preparation kit (PIPseq)

	c) treatment group (this sample in from the control group)

	d) sample number (S1 is for the first sequencing run)

	e) lane number (multiple lanes (L001, L002, L003) represent technical splits of the same library)

	f) read number (either R1 or R2 for paired-end reads)

	g) final segment, which is always 001

File: UW-SCC185_ctrl_S251.zip

Description: Contains 4 individual fastq files

• 2023-12-11-pip-ctrl_S251_L001_R1_001.fastq.gz
• 2023-12-11-pip-ctrl_S251_L001_R2_001.fastq.gz
• 2023-12-11-pip-ctrl_S251_L002_R1_001.fastq.gz
• 2023-12-11-pip-ctrl_S251_L002_R2_001.fastq.gz

Using the naming strategy a-b-c_d_e_f_g.fastq.gz	

	a) sample submission date

	b) library preparation kit (PIPseq)

	c) treatment group (this sample in from the control group)

	d) sample number (S251 is for the second sequencing run to obtain amount of reads requested)

	e) lane number (multiple lanes (L001, L002, L003) represent technical splits of the same library)

	f) read number (either R1 or R2 for paired-end reads)

	g) final segment, which is always 001

File: UW-SCC185_ctx_S3.zip

Description: Contains 6 individual fastq files

• 2023-12-11-pip-ctx_S3_L001_R1_001.fastq.gz
• 2023-12-11-pip-ctx_S3_L001_R2_001.fastq.gz
• 2023-12-11-pip-ctx_S3_L002_R1_001.fastq.gz
• 2023-12-11-pip-ctx_S3_L002_R2_001.fastq.gz
• 2023-12-11-pip-ctx_S3_L003_R1_001.fastq.gz
• 2023-12-11-pip-ctx_S3_L003_R2_001.fastq.gz

Using the naming strategy a-b-c_d_e_f_g.fastq.gz	

	a) sample submission date

	b) library preparation kit (PIPseq)

	c) treatment group (this sample in from the cetuximab-treated group)

	d) sample number (S3 is for the first sequencing run)

	e) lane number (multiple lanes (L001, L002, L003) represent technical splits of the same library)

	f) read number (either R1 or R2 for paired-end reads)

	g) final segment, which is always 001

File: UW-SCC185_ctx_S253.zip

Description: Contains 4 individual fastq files

• 2023-12-11-pip-ctx_S253_L001_R1_001.fastq.gz
• 2023-12-11-pip-ctx_S253_L001_R2_001.fastq.gz
• 2023-12-11-pip-ctx_S253_L002_R1_001.fastq.gz
• 2023-12-11-pip-ctx_S253_L002_R2_001.fastq.gz

Using the naming strategy a-b-c_d_e_f_g.fastq.gz	

	a) sample submission date

	b) library preparation kit (PIPseq)

	c) treatment group (this sample in from the cetuximab-treated group)

	d) sample number (S253 is for the second sequencing run to obtain amount of reads requested)

	e) lane number (multiple lanes (L001, L002, L003) represent technical splits of the same library)

	f) read number (either R1 or R2 for paired-end reads)

	g) final segment, which is always 001

Code/software

These FASTQ files can be processed using PIPseekerV3 or any standard scRNA‑seq pipeline (Cell Ranger, STARsolo, Alevin‑fry, etc.) after custom reference creation. A combined human and mouse reference is recommended because these are PDX models.

Human subjects data

The data in this record were generated from patient-derived xenograft (PDX) tissue, not from patient specimens directly. The PDX models represented here (UW-SCC-185 and UW-SCC-194) were established from tumor tissue obtained under a protocol approved by the University of Wisconsin–Madison Health Sciences Institutional Review Board, protocol #2018-1232 and registered at ClinicalTrials.gov (NCT03769311). All donors provided written informed consent for their tissue to be used to generate these models and for research use of data derived from them.

No patient-level data are included in this deposit. The record contains sequencing data and derived expression matrices from xenograft tumor tissue, annotated only by internal model identifiers (UW-SCC-185, UW-SCC-194). No names, medical record numbers, dates, geographic identifiers, or any other identifiers enumerated under the HIPAA Privacy Rule are present, and no clinical or demographic information about the tissue donors is included. The internal model identifiers carry no embedded donor information; any link between model identifier and donor is held separately by the study team under IRB-approved procedures and is neither included in nor derivable from this deposit.
All data in this data set is appropriate for unrestricted public sharing in Dryad, in accordance with the applicable consent, ethical approvals, and institutional requirements. No individual-level human genomic data are included in the submission.