Shennong Public Reprocessed Data Collection 001

Shennong Public Reprocessed Data Collection 001

This Zenodo record contains uniformly reprocessed public single-cell transcriptomics matrices prepared for Shennong.

Project

Project ID: shennong-public-001

Title: Shennong Public Reprocessed Data Collection 001

Processing fields are stored per sample, not at project level, so future collections can mix organisms, references, assays, and pipeline versions.

Contents

shennong_index.json: primary machine-readable index for Shennong APIs.

UPLOAD_RULES.md: upload and indexing rules for this and future Shennong public collections.

manifest.tsv: flat file manifest with source paths, internal ZIP paths, sizes, and checksums.

{study_id}.zip: one ZIP per study. Each ZIP uses {study_id}/{sample_id}/ paths.

Each sample directory contains:

filtered_feature_bc_matrix.h5

raw_feature_bc_matrix.h5

metrics_summary.csv

Processing Field Conventions

pipeline: cellranger

pipeline_version: plain version string, for example 9.0.1

reference: compact identifier {provider}:{release}:{assembly}, for example GENCODE:48:GRCh38.p14

Human-readable rendering for this collection: Cell Ranger v9.0.1 with GENCODE Release 48 (GRCh38.p14).

Studies

AndrewDHildreth2021

Display name: Andrew D. Hildreth et al. 2021
Publication: Single-cell sequencing of human white adipose tissue identifies new cell states in health and obesity
Journal/year: Nature Immunology 2021
DOI: 10.1038/s41590-021-00922-4
GEO: GSE155960, GSE156110
BioProject: PRJNA656213, PRJNA656785
ZIP: AndrewDHildreth2021.zip

ShuaiHe2020

Display name: Shuai He et al. 2020
Publication: Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs
Journal/year: Genome Biology 2020
DOI: 10.1186/s13059-020-02210-0
GEO: GSE159929
BioProject: PRJNA670909
ZIP: ShuaiHe2020.zip

DanielPCaron2025

Display name: Daniel P. Caron et al. 2025
Publication: Multimodal hierarchical classification of CITE-seq data delineates immune cell states across lineages and tissues
Journal/year: Cell Reports Methods 2025
DOI: 10.1016/j.crmeth.2024.100938
GEO: GSE229791
BioProject: PRJNA955827
ZIP: DanielPCaron2025.zip

MarylineFalquet2023

Display name: Maryline Falquet et al. 2023
Publication: Dynamic single-cell regulomes characterize human peripheral blood innate lymphoid cell subpopulations
Journal/year: iScience 2023
DOI: 10.1016/j.isci.2023.107728
GEO: GSE225168, GSE225169
BioProject: PRJNA934478
ZIP: MarylineFalquet2023.zip

NataliaJaeger2024

Display name: Natalia Jaeger et al. 2024
Publication: Diversity of group 1 innate lymphoid cells in human tissues
Journal/year: Nature Immunology 2024
DOI: 10.1038/s41590-024-01885-y
GEO: GSE240441
BioProject: PRJNA1003807
ZIP: NataliaJaeger2024.zip

CDominguezConde2022

Display name: Cecilia Dominguez Conde et al. 2022
Publication: Cross-tissue immune cell analysis reveals tissue-specific features in humans
Journal/year: Science 2022
DOI: 10.1126/science.abl5197
ArrayExpress/ENA: E-MTAB-11536
ZIP: CDominguezConde2022.zip

Notes

This record does not include FASTQ files, molecule_info.h5, BAM files, or other Cell Ranger output files. The uploaded matrices were regenerated from public sequencing data; cite the original publications and accessions when reusing these data.