CITESeq Processed Data Annotation Template
A data contributor template outlining metadata to be collected as file annotations for CITE-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 |
| assay | The technology used to generate the data in this file. For multimodal datasets with concomitant profiling of biospecimen select all assays that apply. e.g., the GEX files from a CITE-seq experiment should be labeled with both 'scRNASeq' and 'CITESeq'. Multiple selections can be provided in a comma-delimited list. | TRUE | ASAPSeq, ATACSeq, CE-MS, CITESeq, CosMX, CyTOF, GenePS SeqFISH, H&E, LC-MS/MS, NULISA, Not Applicable, Olink Explore HT, Olink Flex, Olink Focus, Olink Reveal, Olink Target 48, Olink Target 96, RNASeq, SNP array, SomaScan, VDJSeq, Visium, WES, WGS, Xenium, feature barcode sequencing, flow cytometry, imaging mass cytometry, imaging mass spectrometry, kiloplex, multiplexed ELISA, scRNASeq, scVDJSeq, serial IHC, snATACSeq, snRNASeq |
| 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 |