scHNSCC_49_PBMC

Download processed single-cell RNA-seq data for this sample

Dataset Information

scHNDB ID

scHNSCC_49_PBMC

Tissue Type

PBMC

Age

66

Gender

F

Position

Floor of Mouth

Clinical Stage

IV

Download Resources

Raw Data Files

Complete single-cell RNA sequencing data in standard 10X Genomics format

10X Raw Data Package

File: scHNSCC_49_PBMC_10x_raw_package.zip

Format: ZIP

Description: Contains barcodes/features/matrix/metadata in standard 10X format

Zenodo download link pending upload.

10X format (4 files)

Files (typically included in the ZIP package above):

  • scHNSCC_49_PBMC_barcodes.tsv.gz
  • scHNSCC_49_PBMC_features.tsv.gz
  • scHNSCC_49_PBMC_matrix.mtx.gz
  • scHNSCC_49_PBMC_metadata.csv.gz

Use Read10X() / sc.read_10x_mtx() on the folder containing barcodes, features, and matrix.

Feature File

File: scHNSCC_49_PBMC_features.tsv.gz

Format: TSV.GZ

Description: Gene features and annotations

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Matrix File

File: scHNSCC_49_PBMC_matrix.mtx.gz

Format: MTX.GZ

Description: Sparse expression matrix

Download

Metadata File

File: scHNSCC_49_PBMC_metadata.csv.gz

Format: CSV.GZ

Description: Cell-level metadata and annotations

Download

Usage Instructions

These files are compatible with standard single-cell analysis tools. To load the data:

In R (Seurat):

library(Seurat)
data <- Read10X(data.dir = "path/to/extracted/files")
seurat_obj <- CreateSeuratObject(counts = data)

In Python (Scanpy):

import scanpy as sc
adata = sc.read_10x_mtx('path/to/extracted/files')