Dataset DOI: 10.5061/dryad.bvq83bknp

Description of the data and file structure

This dataset contains single-cell RNA sequencing (scRNA-seq) data supporting the published article, "Ovarian hormone deficiency enhances wood smoke-induced immune dysfunction via transcriptomic and metabolic alterations."

This study was designed to investigate how acute wood smoke (WS) exposure alters the bone marrow immune landscape in ovariectomized (OVX) C57BL/6 mice under conditions of ovarian hormone deficiency. Mice were exposed to either filtered air (FA) as a control or wood smoke (WS) for 4 hours per day for two consecutive days. Bone marrow was harvested 24 hours after the final exposure.

The experimental groups are as follows:

• OVX-FA: Ovariectomized mice exposed to filtered air (n = 3)
• OVX-WS: Ovariectomized mice exposed to wood smoke (n = 3)

This Dryad deposit contains raw FASTQ files and processed .h5 filtered feature-barcode count matrices generated from this experiment.

Please note: Other data presented in the manuscript, such as the bone marrow-derived macrophage (BMDM) functional assays (metabolic profiling and RT-qPCR), are not included in this dataset.

Files and variables

This dataset includes raw sequencing data (FASTQ) and processed count matrices (.h5 format) for each of the 6 samples. Each .h5 file is a filtered feature-barcode count matrix generated by Cell Ranger. It contains the gene/feature identifiers, cell barcodes, and sparse UMI count matrix for one biological replicate, and can be imported into Seurat or other standard single-cell RNA-seq analysis tools. Below is the complete list of files.

• Sample: OVX_FA_1 (Filtered Air, replicate 1)
  • OVX_FA_1_S3_L004_R1_001.fastq.gz
  • OVX_FA_1_S3_L004_R2_001.fastq.gz
  • OVX_FA_1_sample_filtered_feature_bc_matrix.h5
• Sample: OVX_FA_2 (Filtered Air, replicate 2)
  • OVX_FA_2_S4_L004_R1_001.fastq.gz
  • OVX_FA_2_S4_L004_R2_001.fastq.gz
  • OVX_FA_2_sample_filtered_feature_bc_matrix.h5
• Sample: OVX_FA_3 (Filtered Air, replicate 3)
  • OVX_FA_3_S5_L004_R1_001.fastq.gz
  • OVX_FA_3_S5_L004_R2_001.fastq.gz
  • OVX_FA_3_sample_filtered_feature_bc_matrix.h5
• Sample: OVX_WS_1 (Wood Smoke, replicate 1)
  • OVX_WS_1_S6_L004_R1_001.fastq.gz
  • OVX_WS_1_S6_L004_R2_001.fastq.gz
  • OVX_WS_1_sample_filtered_feature_bc_matrix.h5
• Sample: OVX_WS_2 (Wood Smoke, replicate 2)
  • OVX_WS_2_S7_L004_R1_001.fastq.gz
  • OVX_WS_2_S7_L004_R2_001.fastq.gz
  • OVX_WS_2_sample_filtered_feature_bc_matrix.h5
• Sample: OVX_WS_3 (Wood Smoke, replicate 3)
  • OVX_WS_3_S8_L004_R1_001.fastq.gz
  • OVX_WS_3_S8_L004_R2_001.fastq.gz
  • OVX_WS_3_sample_filtered_feature_bc_matrix.h5

Code/software

The raw data were processed using the 10x Genomics Cell Ranger software to generate filtered feature-barcode count matrices by aligning reads to the mouse reference genome (mm39). Subsequent analysis was performed using the Seurat package (v4.3 or later) in R. Data visualization was performed using GraphPad Prism and Morpheus.

Access information

Other publicly accessible locations of the data:

• None

Data were derived from the following sources:

• Primary data generated for this study