kmmuleelab/P2Mdb

A curated collection of single-cell and bulk transcriptomic datasets from primary tumors and metastases

P2M.db is a curated collection of single-cell and bulk transcriptomic datasets from primary tumors and metastases, with specimen metadata, cell annotations and analysis results. The data were collected from GEO, ArrayExpress and TCGA.

The collection contains 50 single-cell datasets (3,650,286 cells) and 86 bulk datasets (12,896 expression profiles), covering 49 cancer types and subtypes, 28 primary tissues and 25 metastatic tissues.

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Figure 1. Overview of the transcriptomic collection, cancer coverage, deposited records, specimen roles and data access.

Search strategy and metadata screening

The separate GEO searches used a publication-date cutoff of 12 October 2026 and were executed on 13 October 2026. Series and GSM metadata were screened by assay modality, with targeted checks of ambiguous sample descriptions. The PubMed search was performed on 12 October 2026.

GEO single-cell search

326 Series records

(gse[ETYP] AND Homo sapiens[ORGN] AND RNA AND primary AND (metastasis OR metastatic) AND (tumor OR tumour OR cancer OR carcinoma OR neoplasm OR neoplastic) AND ("Expression profiling by high throughput sequencing"[GTYP] OR "Expression profiling by array"[GTYP]) AND ("1900/01/01"[PDAT] : "2026/10/12"[PDAT])) AND ("single cell" OR "single-cell" OR "single nucleus" OR "single-nucleus" OR "scRNA-seq" OR scRNAseq OR "snRNA-seq" OR snRNAseq)

GEO bulk RNA-seq/microarray search

1,565 Series records

(gse[ETYP] AND Homo sapiens[ORGN] AND RNA AND primary AND (metastasis OR metastatic) AND (tumor OR tumour OR cancer OR carcinoma OR neoplasm OR neoplastic) AND ("Expression profiling by high throughput sequencing"[GTYP] OR "Expression profiling by array"[GTYP]) AND ("1900/01/01"[PDAT] : "2026/10/12"[PDAT])) AND ("bulk RNA" OR "bulk RNA-seq" OR "bulk RNA sequencing" OR "RNA-seq" OR RNAseq OR "RNA sequencing" OR microarray OR "Expression profiling by array"[GTYP])

PubMed search

9,822 publication records, counted separately from GEO Series

RNA AND primary AND (metastasis OR metastatic) AND (tumor OR tumour OR cancer OR carcinoma OR neoplasm OR neoplastic) AND Humans[MeSH Terms] AND ("1900/01/01"[Date - Publication] : "2026/10/12"[Date - Publication])

The two GEO searches overlap by 272 accessions and contain 1,619 unique accessions in total. Their counts are not additive.

Accession-level screening records and exclusion summaries are available in the screening directory.

Key regular expressions used for metadata screening

sc_label = '\\b[sn]c?RNA[-_ ]?seq\\b|\\bscRNAseq\\b|\\bsnRNAseq\\b|single[-_ ]?(?:cell|nucle(?:us|i)).{0,35}(?:RNA|transcriptom|gene expression)|(?:RNA|cDNA).{0,30}(?:from|of) (?:a )?single cell|isolated single cell|\\bEasy[-_ ]?Sci[-_ ]?RNA\\b'
sc_platform = '10[xX][-_ ]?genomic|10[xX].{0,25}(?:genomics|chromium)|chromium.{0,60}(?:RNA|gene expression|single cell)|\\bDrop[-_ ]?seq\\b|\\binDrop\\b|\\bCEL[-_ ]?seq|\\bMARS[-_ ]?seq\\b|\\bSeekOne\\b|\\bsnPATHOseq\\b|\\bEasy[-_ ]?Sci[-_ ]?RNA\\b|\\bBD Rhapsody\\b|\\bParse Biosciences\\b|\\bSPLiT[-_ ]?seq\\b'
bulk_protocol = 'TruSeq.{0,80}(?:RNA|mRNA)|NEBNext.{0,80}(?:Ultra|RNA)|NEB.{0,30}Ultra.{0,45}RNA|total RNA librar|RNA librar.{0,35}(?:Ribo[-_ ]?Zero|poly[-_ ]?A)|\\bHTG (?:EdgeSeq|Whole Transcriptome)|\\bmcSCRBseq\\b'
model_pattern = 'xenograft|\\bPDX\\b|\\bPDOX\\b|\\bPDO\\b|\\bMDO\\b|organoid|\\bcell[-_ ]?lines?\\b|\\bcultured\\b|\\bin vitro\\b|\\b(?:cell|tumou?r|melanoma|melanocyte) cultures?\\b|\\bnude mice\\b'
line_pattern = '\\b(?:MDA[ _-]?MB[ _-]?\\d+|MDA231|MCF[ _-]?7|HCT[ _-]?116|SW[ _-]?(?:480|620)|HT[ _-]?29|A549|HeLa|U2OS|DU[ _-]?145|PC[ _-]?3|LNCaP|C4[ _-]?2\\w*|HCC1806|SUM159\\w*|4T1|H1299|H1975|H358|HepG2|Huh7|U87[-_ ]?MG|786[-_ ]?O|ACHN|MIA[-_ ]?PaCa[-_ ]?2|PANC[-_ ]?1|T47D|BT(?:20|474|549)|TOV21G|SiHa|BHT101|A375|A2058|SKOV3|OVCAR\\d+|FaDu|HOS|MG63|HMLE|HMLER|LOVO|DLD1|SKBR3|WM239A?|113/6-4L|131/4-5B[12]|143B|MM\\.1S|OPM2|CAL27|CAL33|RM82|TC71|NCI[-_ ]?H\\d+)\\b'

The complete matching patterns are provided in screening/regex.md.

Data files

Datasets are organized by their original study accession under scRNA-seq/ and bulk/.

Expression data are provided in two formats: RDS files and CSV files packaged in RAR archives. Both formats include the expression data and corresponding cell or sample metadata.

File or directory	Contents
.rds	Expression data and metadata; single-cell objects also contain available cell annotations
<accession>_expression.rar	RAR archive containing expression.csv and metadata.csv
samples.csv	Sample identifiers, specimen classifications and associated metadata
dataset.csv	Study information, data source, annotation methods and processing notes
qc.csv	Quality control measurements
processing_parameters.csv	Processing settings in three columns: function, parameter, value
analysis/	Available differential expression, enrichment and other analysis results

Each expression RAR contains expression.csv (features in rows; cells or samples in columns) and metadata.csv. Metadata rows follow the expression column order and retain specimen labels and available cell annotations. Single-cell exports use the stored RNA counts layer when available, otherwise the stored expression data layer; expression_layer identifies the selection. Bulk expression values retain their recorded scale. Studies with multiple bulk matrices contain a separate CSV pair for each platform. Missing values are written as NA.

Available analyses differ among datasets. analysis/comparisons.csv identifies the specimen groups, metastatic sites and annotation methods used in each comparison.

At the repository root, sources.csv records study sources and the evidence for specimen labels and annotations. files.csv lists file paths and sizes, and qc_fields.csv defines QC fields. Collection statistics are in statistics/.

Read the data

Read RDS files directly in R, or extract the RAR archive before reading its CSV files:

object <- readRDS("path/to/file.rds")
metadata <- read.csv("path/to/metadata.csv", check.names = FALSE)

For examples that select specimens and handle bulk objects with multiple matrices, see code/read_data.R and code/README.md. Analysis scripts and their documentation are in code/. The original P2M.Rcode analysis scripts are mirrored in code/analysis/ with standardized filenames and unchanged contents.

Use of the data

Check the specimen labels and comparison definitions before analysis. Metastatic tissue samples and TCGA clinical M0/M1 groups represent different comparisons. Some datasets also contain normal, fluid or unclassified specimens. Sample counts are not necessarily counts of independent patients.

Some historical analysis tables lack complete input sample records; the dataset-specific limitations are recorded in sources.csv and dataset.csv. The 20 TCGA expression releases contain TPM values; the bulk analysis workflows use log2(TPM + 1). QC summaries describe the released matrices or the recorded filtering stages. Unavailable measurements and annotations are represented by NA or empty fields.

Data use and citation

The curated metadata, QC summaries and analysis results generated for P2M.db are licensed under CC BY 4.0. Original expression data and source annotations retain their source terms; code and reference resources retain their own licenses. See LICENSE for the scope.

Cite this repository and the original studies listed in sources.csv, and record the repository revision used in your analysis.