scRNASeq Level 1 File Annotations Template

A template for collecting file-level metadata for scRNA-seq fastq files (i.e., level 1 data).

Attribute	Description	Required	Valid Values
assay	The technology used to generate the data.	TRUE	scRNASeq, RNASeq, WES, WGS, LC-MS/MS, CyTOF
assay_metadata_synID	The synID scRNA-seq assay metadata file corresponding to this data file.	FALSE
biospecimen_metadata_synID	The synID biospecimen metadata file containing information about the samples profiled	FALSE
data_level	The processing level of the data.	TRUE	1, 2, 3, 4
data_type	High-level classification of the type of data contained in the file, loosely related to the experimental method or biological entity that is being profiled.	TRUE	transcriptomics, proteomics, genomics, metabolomics, lipidomics, microbiome, cytometry, functional study
file_format	Defined format of the data file, typically corresponding to extension, but sometimes indicating more general group of files produced by the same tool or software	TRUE	fastq, bam, csv, xlsx, txt, pdf, tsv, .h5, tar.gz, .h5ad
resource_type	The type of resource being stored and annotated	TRUE	experimental data, metadata, report
sample_id	Unique sample identifier, formatted as `'individual_id'_'participant_id'_'collection_num'_'type_key'_'sample_num'`	TRUE
specimen_modality	Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens	TRUE	single specimen, multispecimen