Attribute Manifest Name Description Required Conditional If Data Type Valid Values Xenium Bundle Contents 10X Genomics Xenium ISS Experiment A comma separated list of filenames within the Xenium bundle zip file TRUE String Decoded Transcripts 10X Genomics Xenium ISS Experiment "In Xenium, this is the number of high-quality, decoded-to-gene nuclear transcripts divided by the total segmented nuclear area to get a transcript density (units are reported in 100um^2)." TRUE String Xenium IF image HTAN File ID 10X Genomics Xenium ISS Experiment The HTAN Data File ID of a Imaging Level 2 file FALSE String Xenium HE image HTAN File ID 10X Genomics Xenium ISS Experiment The HTAN Data File ID of a Imaging Level 2 file FALSE String Panel Name "10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" "The human-readable panel name. This could be the Gene Panel name or Protein Panel name. In Xenium, this refers to the string entered as the name in panel specification (e.g. Xenium Human Immuno-Oncology Add-on B Gene Expression). In CosMx, this refers to the panel name as it appears in the CosMx catalog (e.g. CosMx Human Universal Cell Characterization Panel (1000-plex))" TRUE String Total Number of Cells "10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" The total number of cells analyzed on the flow cell TRUE String Total Number of Targets "10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" Refers to the target of an assay. Can be genes/transcripts or probes TRUE String Experiment IF Channels "10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" "A comma-separated list with any number of channels the user deems appropriate(Example: PanCK, CD45, CD3, DAPI)" TRUE String Transcripts per Cell "10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" Mean or Median transcript count per cell analyzed on the flow cell or slide TRUE String Percent of Transcripts within Cells "10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" The percentage of transcripts assigned to assayed cells TRUE String Surface area "10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" "Surface area of the ROI in square microns (µm^2). In CosMx, this is referred to as the Scan Area. In Xenium, this is referred to as the Region Area" TRUE String ROI name "10X Genomics Xenium ISS Experiment,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" ROI name (application generated). For Xenium this is referred to as the “region name” TRUE String Slide Version 10x Visium Spatial Transcriptomics - RNA-seq Level 1 Version of imaging slide used. Slide version is critical for the analysis of the sequencing data as different slides have different capture area layouts. FALSE String V1 V2 V3 V4 Image Re-orientation 10x Visium Spatial Transcriptomics - RNA-seq Level 1 "To ensure good fiducial alignment and tissue spots detection, it is important to correct for this shift in orientation." FALSE String TRUE FALSE Permeabilization Time 10x Visium Spatial Transcriptomics - RNA-seq Level 1 Fixed and stained tissue sections are permeabilized for different times. Each Capture Area captures polyadenylated mRNA from the attached tissue section. Measure is provided in minutes. FALSE String RIN 10x Visium Spatial Transcriptomics - RNA-seq Level 1 A numerical assessment of the integrity of RNA based on the entire electrophoretic trace of the RNA sample including the presence or absence of degradation products. Number FALSE String DV200 10x Visium Spatial Transcriptomics - RNA-seq Level 1 Represents the percentage of RNA fragments that are >200 nucleotides in size. Number FALSE String cDNA 10x Visium Spatial Transcriptomics - RNA-seq Level 1 "Complementary DNA. A DNA copy of an mRNA or complex sample of mRNAs, made using reverse transcriptase" FALSE String Feature barcoding 10x Visium Spatial Transcriptomics - RNA-seq Level 1 A method for adding extra channels of information to cells by running single-cell gene expression in parallel with other assays [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/feature-bc] FALSE String cDNA Offset 10x Visium Spatial Transcriptomics - RNA-seq Level 1 Offset in sequence for cDNA read (in bp): number TRUE "Spatial Read2 is ""cDNA""" String cDNA Length 10x Visium Spatial Transcriptomics - RNA-seq Level 1 Length of cDNA read (in bp): number TRUE "Spatial Read2 is ""cDNA""" String Feature Reference Id 10x Visium Spatial Transcriptomics - RNA-seq Level 1 "Unique ID for this feature. Must not contain whitespace, quote or comma characters. Each ID must be unique and must not collide with a gene identifier from the transcriptome [https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis#feature-ref]" TRUE "Reverse Transcription Primer is ""Feature barcoding""" String Protocol Link "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment,Slide-seq Level 1" "Protocols.io ID or DOI link to a free/open protocol resource describing in detail the assay protocol (e.g. surface markers used in Smart-seq, dissociation duration, lot/batch numbers for key reagents such as primers, sequencing reagent kits, etc.) or the protocol by which the sample was obtained or generated." TRUE String Slide ID "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10x Visium Spatial Transcriptomics - Auxiliary Files,10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" "For Visium, it is the unique identifier printed on the label of each Visium slide. The serial number starts with V followed by a number which can range between one through five and ends with a dash and a three digit number, such as 123. For CosMx, this refers to the loaded Flow Cell ID. For Xenium, this ID indicates the slide orientation, as it matches the relative location of the ID on the physical Xenium slide." FALSE String Capture Area "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - Auxiliary Files" "Area (or Capture Area) - One of the either four or two active regions where tissue can be placed on a Visium slide. Each area is intended to contain only one tissue sample. Slide areas are named consecutively from top to bottom: A1, B1, C1, D1 for Visium slides with 6.5 mm Capture Area and A, B for CytAssist slides with 11 mm Capture Area. Both CytAssist slides with 6.5 mm Capture Area and Gateway Slides contain only two slide areas, A1 and D1." FALSE String A B C D A1 B1 C1 D1 Filename "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,NanoString GeoMx DSP Spatial Transcriptomics Level 1,NanoString GeoMx DSP Spatial Transcriptomics Level 3,10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment,Slide-seq Level 1,Slide-seq Level 2,Slide-seq Level 3" Name of a file TRUE String Run ID "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,Slide-seq Level 3" A unique identifier for this individual run (typically associated with a single slide) of the spatial transcriptomic processing workflow. TRUE String File Format "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,NanoString GeoMx DSP Spatial Transcriptomics Level 1,NanoString GeoMx DSP Spatial Transcriptomics Level 3,10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment,Slide-seq Level 1,Slide-seq Level 2,Slide-seq Level 3" "Format of a file (e.g. txt, csv, fastq, bam, etc.)" TRUE String hdf5 bedgraph idx idat bam bai excel powerpoint tif tiff OME-TIFF png doc pdf fasta fastq sam vcf bcf maf bed chp cel sif tsv csv txt plink bigwig wiggle gct bgzip zip seg html mov hyperlink svs Md flagstat gtf raw msf rmd bed narrowPeak bed broadPeak bed gappedPeak avi pzfx fig xml tar R script abf bpm dat jpg locs Sentrix descriptor file Python script sav gzip sdf RData hic ab1 7z gff3 json sqlite svg sra recal tranches mtx tagAlign dup DICOM czi mex cloupe Am cell am mpg M mzML scn dcc rcc pkc sf bedpe HTAN Parent Biospecimen ID "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,NanoString GeoMx DSP Spatial Transcriptomics Level 1,NanoString GeoMx DSP Spatial Transcriptomics Level 3,10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment,Slide-seq Level 1,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" HTAN Biospecimen Identifier (eg HTANx_yyy_zzz) indicating the biospecimen(s) from which these files were derived; multiple parent biospecimen should be comma-separated TRUE "Is lowest level is ""Yes - Is lowest level""" String HTAN Data File ID "10x Visium Spatial Transcriptomics - RNA-seq Level 1,10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,NanoString GeoMx DSP Spatial Transcriptomics Level 1,NanoString GeoMx DSP Spatial Transcriptomics Level 3,10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment,Slide-seq Level 1,Slide-seq Level 2,Slide-seq Level 3" Self-identifier for this data file - HTAN ID of this file HTAN ID SOP (eg HTANx_yyy_zzz) TRUE String Read Indicator "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" "Indicate if this is Read 1 (R1), Read 2 (R2), Index Reads 1 (I1), Index Reads 2 (I2), or Other" TRUE String R1 R2 R1&R2 I1 I2 Other Spatial Read1 "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" Read 1 content description TRUE String cDNA Spatial Barcode and UMI Spatial Read2 "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" Read 2 content description TRUE String cDNA Spatial Barcode and UMI Spatial Library Construction Method "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" Process which results in the creation of a library from fragments of DNA using cloning vectors or oligonucleotides with the role of adaptors [OBI_0000711] TRUE String Smart-seq2 Smart-SeqV4 10xV1.0 10xV1.1 10xV2 10xV3 10xV3.1 Drop-seq inDropsV2 inDropsV3 TruDrop Nextera XT Library Preparation Days from Index "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" Number of days between sample for assay was received in lab and the libraries were prepared for sequencing [number]. If not applicable please enter 'Not Applicable' FALSE String Sequencing Library Construction Days from Index "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" Number of days between sample for assay was received in lab and day of sequencing library construction [number]. If not applicable please enter 'Not Applicable' TRUE String End Bias "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" "The end of the cDNA molecule that is preferentially sequenced, e.g. 3/5 prime tag/end or the full length transcript" TRUE String 3 Prime 5 Prime Full Length Transcript Reverse Transcription Primer "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" "An oligo to which new deoxyribonucleotides can be added by DNA polymerase [SO_0000112]. The type of primer used for reverse transcription, e.g. oligo-dT or random primer. This allows users to identify content of the cDNA library input e.g. enriched for mRNA" TRUE String Oligo-dT Poly-dT Feature barcoding Random Sequencing Platform "10x Visium Spatial Transcriptomics - RNA-seq Level 1,Slide-seq Level 1" A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument. TRUE String Illumina Next Seq 500 Illumina Next Seq 550 Illumina Next Seq 2500 Illumina NovaSeq 6000 Illumina MiSeq 454 GS FLX Titanium AB SOLiD 4 AB SOLiD 2 AB SOLiD 3 Complete Genomics Illumina HiSeq X Ten Illumina HiSeq X Five Illumina Genome Analyzer II Illumina Genome Analyzer IIx Illumina HiSeq 2000 Illumina HiSeq 2500 Illumina HiSeq 4000 Illumina NextSeq Ion Torrent PGM Ion Torrent Proton Ion Torrent S5 PacBio RS NovaSeq 6000 NovaSeqS4 Ultima Genomics UG100 Oxford Nanopore minION GridION PromethION PacBio Sequel2 Revio Illumina NextSeq 1000 Illumina NextSeq 2000 Other unknown Not Reported Whitelist Spatial Barcode File Link 10x Visium Spatial Transcriptomics - RNA-seq Level 2 Link to file listing all possible spatial barcodes. URL TRUE String Yes - Applied Hard Trimming 10x Visium Spatial Transcriptomics - RNA-seq Level 2 Hard Trimming was applied FALSE String Aligned Read Length 10x Visium Spatial Transcriptomics - RNA-seq Level 2 Read length used for alignment if hard trimming was applied TRUE "Applied Hard Trimming is ""Yes - Applied Hard Trimming""" String HTAN Parent Data File ID "10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,Slide-seq Level 2,Slide-seq Level 3" HTAN Data File Identifier indicating the file(s) from which these files were derived TRUE String Workflow Version "10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,Slide-seq Level 2,Slide-seq Level 3" Major version of the workflow (e.g. Cell Ranger v3.1) TRUE String Workflow Link "10x Visium Spatial Transcriptomics - RNA-seq Level 2,10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - RNA-seq Level 4,10x Visium Spatial Transcriptomics - Auxiliary Files,Slide-seq Level 2,Slide-seq Level 3" Link to workflow or command. DockStore.org recommended. URL TRUE "Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""" String Checksum "10x Visium Spatial Transcriptomics - RNA-seq Level 2,Slide-seq Level 2" MD5 checksum of the BAM file TRUE String UMI Tag "10x Visium Spatial Transcriptomics - RNA-seq Level 2,Slide-seq Level 2" "SAM tag for the UMI field; please provide a valid UB, UMI (e.g. UB:Z or UR:Z)" TRUE String Spatial Barcode Tag "10x Visium Spatial Transcriptomics - RNA-seq Level 2,Slide-seq Level 2" SAM tag for spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) TRUE String Applied Hard Trimming "10x Visium Spatial Transcriptomics - RNA-seq Level 2,Slide-seq Level 2" Was Hard Trimming applied TRUE String Yes - Applied Hard Trimming no Genomic Reference "10x Visium Spatial Transcriptomics - RNA-seq Level 2,Slide-seq Level 2" Exact version of the human genome reference used in the alignment of reads (e.g. GCF_000001405.39) TRUE "Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""" String Genomic Reference URL "10x Visium Spatial Transcriptomics - RNA-seq Level 2,Slide-seq Level 2" Link to human genome sequence (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz) TRUE "Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""" String Genome Annotation URL "10x Visium Spatial Transcriptomics - RNA-seq Level 2,Slide-seq Level 2" Link to the human genome annotation (GTF) file (e.g. ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz) TRUE String Spots under tissue 10x Visium Spatial Transcriptomics - RNA-seq Level 3 The number of barcodes associated with a spot under tissue. TRUE String Mean Reads per Spatial Spot 10x Visium Spatial Transcriptomics - RNA-seq Level 3 "The number of reads, both under and outside of tissue, divided by the number of barcodes associated with a spot under tissue." TRUE String Proportion Reads Mapped 10x Visium Spatial Transcriptomics - RNA-seq Level 3 Proportion of mapped reads collected from samtools. Number FALSE String Proportion Reads Mapped to Transcriptome 10x Visium Spatial Transcriptomics - RNA-seq Level 3 Fraction of reads that mapped to a unique gene in the transcriptome. The read must be consistent with annotated splice junctions. These reads are considered for UMI counting. TRUE String Visium File Type "10x Visium Spatial Transcriptomics - RNA-seq Level 3,10x Visium Spatial Transcriptomics - Auxiliary Files" The file type generated for the visium experiment. TRUE String reference png reference jpg json scale factors probe dataset csv qc result html filtered mex unfiltered mex tissue_positions barcodes features fiducial image png fiducial image jpg detected image png detected jpg high res image low res image Sequencing Saturation "10x Visium Spatial Transcriptomics - RNA-seq Level 3,NanoString GeoMx DSP ROI DCC Segment Annotation Metadata" "The fraction of reads originating from an already-observed UMI. This is a function of library complexity and sequencing depth. More specifically, this is the fraction of confidently mapped, valid spot-barcode, valid UMI reads that had a non-unique (spot-barcode, UMI, gene)." TRUE String Median Number Genes per Spatial Spot "10x Visium Spatial Transcriptomics - RNA-seq Level 3,Slide-seq Level 3" The median number of genes detected per spot under tissue-associated barcode. Detection is defined as the presence of at least 1 UMI count. TRUE String Median UMI Counts per Spot "10x Visium Spatial Transcriptomics - RNA-seq Level 3,Slide-seq Level 3" The median number of UMI counts per tissue covered spot. TRUE String Visium Workflow Type 10x Visium Spatial Transcriptomics - RNA-seq Level 4 Generic name for the workflow used to analyze the visium data set. TRUE String Visium Workflow Parameters Description 10x Visium Spatial Transcriptomics - RNA-seq Level 4 Parameters used to run the workflow.. TRUE String CosMx Bundle Contents Nanostring CosMx SMI Experiment A comma separated list of filenames within the CosMx bundle zip file TRUE String CosMx Assay Type Nanostring CosMx SMI Experiment The specification for barcodes on each image. Either RNA probe or protein antibody according to the assay TRUE String RNA protein Number of FOVs Nanostring CosMx SMI Experiment The total number of FOVs recorded for the sample on a single flow cell TRUE String Mean Total Transcripts per Area Nanostring CosMx SMI Experiment The mean total transcripts per um3 TRUE String Unique Genes Nanostring CosMx SMI Experiment The total unique genes detected above background FALSE String Total Negative Probe Counts Nanostring CosMx SMI Experiment Mean Total Negative probe counts/cell TRUE String Slide name NanoString GeoMx DSP ROI DCC Segment Annotation Metadata "Similar to a Run ID, the slide name indicates the slide a given ROI is linked to (as reported in Segment Summary)." FALSE String MapQ30 NanoString GeoMx DSP ROI DCC Segment Annotation Metadata Number of reads with Quality >= 30. FALSE String Raw reads NanoString GeoMx DSP ROI DCC Segment Annotation Metadata Reads not yet analyzed in any way to be used for data analysis. The number of reads that pass filter from the flow cell represented in the FASTQ file. FALSE String Stitched reads NanoString GeoMx DSP ROI DCC Segment Annotation Metadata "Represents consensus from the overlapping sequence of read 1 and 2. This is a % of the aligned reads that were overlapped and consensus confirmed, usually upward of 80% but less in terms of number of reads than aligned reads" FALSE String Aligned reads NanoString GeoMx DSP ROI DCC Segment Annotation Metadata Is a sequence that has been aligned to a gene/probe. Typically these reads can number from the hundreds of thousands to tens of millions. In GeoMx alignment is via mapping the RTS ID to a white list of sequences that represent targets. FALSE String Deduplicated reads NanoString GeoMx DSP ROI DCC Segment Annotation Metadata Is the replacement of blocks of duplicate data with a Virtual Index Pointer linking the new sub-block to the existing block of data in a duplicate repository. This is used to reduce the amount of space need to store the data. FALSE String In Situ Negative median NanoString GeoMx DSP ROI DCC Segment Annotation Metadata Is the median of all negative control probes for a given segment. A measure of signal to background for each segment. FALSE String Biological probe median NanoString GeoMx DSP ROI DCC Segment Annotation Metadata Is the median count from all probes except the negative control probes. A measure of signal to background for each segment FALSE String Scan name "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" GeoMx Scan name (as appears in Segment Summary) TRUE String Segment name "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Name given to segment at time of generation TRUE String ROI X Coordinate "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" X location within the image TRUE String ROI Y Coordinate "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Y location within the image TRUE String Tags "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Unique descriptor of a variable group (ie. MAPK+) TRUE String Scan Height "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Height of the scan for GeoMx Analysis TRUE String Scan Width "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Width of the scan for GeoMx Analysis TRUE String Scan Offset X "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Offset X of the scan for GeoMx Analysis TRUE String Scan Offset Y "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Offset Y of the scan for GeoMx Analysis TRUE String Nuclei count "NanoString GeoMx DSP ROI DCC Segment Annotation Metadata,NanoString GeoMx DSP ROI RCC Segment Annotation Metadata" Number of nuclei detected in the segment (if applicable) TRUE String QC status NanoString GeoMx DSP ROI RCC Segment Annotation Metadata ROI quality control flag as reported by the application FALSE String Binding Density NanoString GeoMx DSP ROI RCC Segment Annotation Metadata The binding density as reported by the application FALSE String Positive norm factor NanoString GeoMx DSP ROI RCC Segment Annotation Metadata The Positive Control Normalization factor calculated using pos-hyb controls FALSE String Tissue Stain NanoString GeoMx DSP ROI RCC Segment Annotation Metadata e.g. CD45 or PanCK (if masking was performed) FALSE String Synapse ID of GeoMx DSP PKC File NanoString GeoMx DSP Spatial Transcriptomics Level 1 The Synapse ID(s) associated with the PKC mapping file for the assay. Multiple files are listed as comma separated values. TRUE String GeoMx DSP NGS Sequencing Platform NanoString GeoMx DSP Spatial Transcriptomics Level 1 A platform is an object aggregate that is the set of instruments and software needed to perform a process [OBI_0000050]. Specific model of the sequencing instrument. FALSE String GeoMx DSP NGS Library Selection Method NanoString GeoMx DSP Spatial Transcriptomics Level 1 How RNA molecules are isolated. FALSE String GeoMx DSP NGS Library Preparation Kit Name NanoString GeoMx DSP Spatial Transcriptomics Level 1 Name of Library Preparation Kit. String FALSE String GeoMx DSP Library Preparation Kit Vendor NanoString GeoMx DSP Spatial Transcriptomics Level 1 Vendor of Library Preparation Kit. String FALSE String GeoMx DSP Library Preparation Kit Version NanoString GeoMx DSP Spatial Transcriptomics Level 1 Version of Library Preparation Kit. String FALSE String Synapse ID of GeoMx Lab Worksheet File NanoString GeoMx DSP Spatial Transcriptomics Level 1 Synapse ID(s) of Lab Worksheet Files output from the GeoMx DSP workflow. Multiple files are listed as comma separated values. FALSE String Software and Version "NanoString GeoMx DSP Spatial Transcriptomics Level 1,10X Genomics Xenium ISS Experiment,Nanostring CosMx SMI Experiment" Name of software used to generate expression values. String TRUE "Pseudo Alignment Used is ""Yes - Pseudo Alignment Used""" String GeoMx DSP Assay Type NanoString GeoMx DSP Spatial Transcriptomics Level 3 The assay type which was used for the GeoMx DSP pipeline. TRUE String RNA nCounter Protein nCounter Protein NGS RNA NGS Synapse ID of GeoMx DSP ROI Segment Annotation File NanoString GeoMx DSP Spatial Transcriptomics Level 3 Synapse ID(s) for ROI/Segmentation annotations in the GeoMx DSP experiment. TRUE String GeoMx DSP Unique Probe Count NanoString GeoMx DSP Spatial Transcriptomics Level 3 Total number of unique probes reported. FALSE String GeoMx DSP Unique Target Count NanoString GeoMx DSP Spatial Transcriptomics Level 3 Total number of unique genes reported. FALSE String GeoMx DSP Genomic Reference NanoString GeoMx DSP Spatial Transcriptomics Level 3 Exact version of the human genome reference used in the alignment of reads (e.g. https://www.gencodegenes.org/human/). Only applicable to some applications in GeoMx FALSE String GeoMx DSP Workflow Type NanoString GeoMx DSP Spatial Transcriptomics Level 3 Generic name for the workflow used to analyze the GeoMx DSP data set. FALSE String GeoMx DSP Workflow Parameter Description NanoString GeoMx DSP Spatial Transcriptomics Level 3 Parameters used to run the GeoMx DSP workflow. FALSE String GeoMx DSP Workflow Link NanoString GeoMx DSP Spatial Transcriptomics Level 3 Link to workflow or command. DockStore.org recommended. URL FALSE String Matrix Type "NanoString GeoMx DSP Spatial Transcriptomics Level 3,Slide-seq Level 3" Type of data stored in matrix. TRUE String Raw Counts Normalized Counts Scaled Counts Batch Corrected Counts Nucleic Acid Source Slide-seq Level 1 The source of the input nucleic molecule TRUE String Single Cell Bulk Whole Cell Single Nucleus Bulk Nuclei Micro-region Spatial Barcode Offset Slide-seq Level 1 Offset in sequence for spot barcode read (in bp): number TRUE "Spatial Read2 is ""Spatial Barcode and UMI""" String Spike In Slide-seq Level 1 A set of known synthetic RNA molecules with known sequence that are added to the cell lysis mix TRUE String ERCC Other Spike In No Spike In PhiX Technical Replicate Group Slide-seq Level 1 A common term for all files belonging to the same cell or library. Provide a numbering of each library prep batch (can differ from encapsulation and sequencing batch) FALSE String Nucleic Acid Capture Days from Index Slide-seq Level 1 Number of days between sample for single cell assay was received in lab and day of nucleic acid capture part of library construction (in number of days since sample received in lab) [number]. If not applicable please enter 'Not Applicable' TRUE String Spatial Barcode Length Slide-seq Level 1 Length of spot barcode read (in bp): number TRUE "Spatial Read2 is ""Spatial Barcode and UMI""" String UMI Barcode Offset Slide-seq Level 1 "Start position of UMI barcode in the sequence. Values: number, 0 for start of read" TRUE "Spatial Read2 is ""Spatial Barcode and UMI""" String UMI Barcode Length Slide-seq Level 1 Length of UMI barcode read (in bp): number TRUE "Spatial Read2 is ""Spatial Barcode and UMI""" String ERCC Slide-seq Level 1 The External RNA Controls Consortium (ERCC) spike in set is commonly used in single-cell experiments for normalization FALSE String Spike In Concentration Slide-seq Level 1 The final concentration or dilution (for commercial sets) of the spike in mix [PMID:21816910] TRUE "Spike In is ""ERCC""" String Spatial Barcode and UMI "Slide-seq Level 1,10x Visium Spatial Transcriptomics - RNA-seq Level 1" Spot and transcript identifiers TRUE String Matched Spatial Barcode Tag Slide-seq Level 2 SAM tag for matched spot barcode field; please provide a valid spot barcode tag (e.g. CB:Z) (Slide-seq specific) TRUE String Slide-seq Workflow Type "Slide-seq Level 2,Slide-seq Level 3" Generic name for the workflow used to analyze the Slide-seq data set. String TRUE String Slide-seq Workflow Parameter Description "Slide-seq Level 2,Slide-seq Level 3" Parameters used to run the Slide-seq workflow. String TRUE String Sequencing Batch ID Slide-seq Level 3 Links samples to a specific local sequencer run. Can be string or 'null' TRUE String Data Category Slide-seq Level 3 Specific content type of the data file. TRUE String Gene Expression Transcript Expression Exon Expression Quantification Gene Expression Quantification Isoform Expression Quantification Splice Junction Quantification Other Beads Total Slide-seq Level 3 Number of sequenced beads. Applies to raw counts matrix only. Integer FALSE String Slide-seq Bead File Type Slide-seq Level 3 The type of Level 3 file submitted as part of the Slide-seq workflow. TRUE String Matrix Features Matrix Barcodes All Bead Locations All Bead Barcodes Matched Bead Barcodes Matched Bead Locations Not Applicable Slide-seq Fragment Size Slide-seq Level 3 Average cDNA length associated with the experiemtn. Integer FALSE String