snATACSeq Processed Data Annotation Template

A data contributor template outlining metadata to be collected as file annotations for snATAC-seq processed data files (i.e., anything not a fastq file)

Instructions

This template collects file-level metadata and curates your file with this critical information thereby enabling discoverability, SQL queries, and overall organization and metrics calculations of your data files.

Attribute	Description	Required	Valid Values
RObjectClass	Rds files store R objects, one per file. This label details the class of the R object saved to the Rds file or other similar file types.	FALSE	ROCR prediction.object, Seurat object, SummarizedExperiment, Symphony reference, data.frame, list, matrix, sparse matrix, vector
biospecimenID	A unique identifier assigned to specimens collected from study participants. For multi-specimen data files provide all IDs in a comma-separated list.	TRUE
cellRangerOutput	10x Genomics Cell Ranger software output several different counts results and formats, some with different processing applied. This label distinguishes between these types and is particularly helpful when multiple files are uploaded with the sample name, e.g., barcodes.tsv.gz	TRUE	Not Applicable, filtered MEX, filtered_feature_bc_matrix, filtered_peak_bc_matrix, raw MEX, raw_feature_bc_matrix, raw_peak_bc_matrix
dataLevel	Level of data processing applied to file. Levels refer to pre-defined standards of processing for the given assay.	TRUE	1, 2, 3, 4, 5, Not Applicable, unknown
fileFormat	Standard file format name or file extension	TRUE	csv, tsv, txt, xlsx, xls, fam, bim, bed, bam, h5, mtx, bai, rds, tgz, zip, h5ad, html
individualID	Unique identifier assigned to each study participant. For multi-specimen data files provide all IDs in a comma-separated list.	TRUE
metadataType	A label further classifying the content of metadata resource.	TRUE	single-cell metadata
processedDataType	A label used for file annotations to provide a brief description of the processed data file. Multiple selections can be provided in a comma-delimited list.	FALSE	barcode counts, differential expression results, epigenomic peaks, gene counts
resourceType	High-level classification of the file content	TRUE	experimental data, metadata
specimenModality	Label assigned to experimental data files indicating whether the data contained corresponds to a single or multiple biospecimens	TRUE	multispecimen, single specimen, unknown