Dataset Card for riken2018_processed

Dataset Summary

This dataset is derived from single-cell RNA-seq of peripheral blood mononuclear cells (PBMCs) from supercentenarians (ages 110+) and younger controls, processed from the study:

Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians
— Hashimoto et al., PNAS (2019)
DOI:10.1073/pnas.1907883116

The final object includes cells from three experimental batches (firstrun, SC1, SC2) and supports aging-focused immunology research.

Transformation Summary

Raw data was downloaded from http://gerg.gsc.riken.jp/SC2018/ and processed with the following steps:

1. Download and Extraction:

   • Retrieved UMI matrix (01.UMI.txt.gz) and cell barcodes (03.Cell.Barcodes.txt.gz).
   • Extracted expression matrices from SC1.tar and SC2.tar using scanpy.read_10x_mtx.

2. UMI Matrix Assembly:

   • Constructed an AnnData object from the UMI count matrix and matched barcodes.
   • Gene names were mapped to Ensembl IDs using SC1 reference.

3. Batch Merging:

   • Merged firstrun, SC1, and SC2 into one AnnData object using scanpy.concat, with batch labels preserved.

4. Metadata Curation:

   • Filled in missing columns for sample origin (SC1, SC2, etc.) based on batch labels.
   • Added standardized columns: age_int, assay_simple, cell_type, and centenarian_status.

5. Output:

   • Saved final object to raw/riken2018/processed/riken2018_processed.h5ad.

Supported Tasks and Benchmarks

• Immune Aging Analysis: Especially suited for studying the immune profile of extreme aging.
• CD4 T Cell Phenotyping: Detects rare CD4 cytotoxic T cell expansions.
• Batch Integration: Includes multiple experimental runs merged with consistent annotations.

Languages

Textual metadata and annotations are in English.

Dataset Structure

Data Instances

Each instance represents a single PBMC with:

• Raw UMI expression data
• Batch origin (firstrun, SC1, SC2)
• Age group metadata (centenarian_status, age_int)
• Cell type label (PBMC)

Data Splits

• No formal train/test split provided. Users may stratify by centenarian_status.

Dataset Creation

Curation Rationale

The dataset was assembled to study cellular aging phenotypes by comparing PBMC populations between centenarians and controls, with a focus on adaptive immunity.

Source Data

• 7 supercentenarians and 5 controls
• Collected and sequenced using 10x Genomics Chromium 3' technology
• Published by RIKEN Center for Integrative Medical Sciences

Preprocessing Details

• Raw count matrix: 01.UMI.txt.gz
• Barcode matching and gene name alignment using 10x SC1 reference
• Minor cleanup of missing metadata and consistent column naming
• Concatenation with scanpy after aligning gene and barcode identifiers

Licensing Information

This dataset is distributed under the Creative Commons BY 4.0 license. Please cite the original paper when using this dataset in publications.

Citation

@article{hashimoto2019supercentenarians,
  title={Single-cell transcriptomics reveals expansion of cytotoxic CD4 T cells in supercentenarians},
  author={Hashimoto, Kosuke and Kouno, Tsukasa and Ikawa, Tomokatsu and et al.},
  journal={Proceedings of the National Academy of Sciences},
  volume={116},
  number={48},
  pages={24242--24251},
  year={2019},
  publisher={National Academy of Sciences}
}