Sc Rnaseq_Assay_Template
VEOIBD Single Cell RNASeq Assay Metadata Template [Source]
Key | Key Description | Type | Valid Values | DependsOn | Required | Source | Module |
---|---|---|---|---|---|---|---|
assay | The technology used to generate the data in this file | STRING | rnaSeq,scrnaSeq | True | NGS | ||
platform | The specific version (manufacturer, model, etc.) of a technology that is used to carry out a laboratory or computational experiment. | STRING | HiSeqX,HiSeq4000,Illumina_1M,HiSeq3000,HiSeq2500,DNBSEQ,HiSeq1000,GAIIx,Illumina_h650,ddSEQ Single-Cell Isolator,confocalImaging,Bruker Avance III,Bionano Irys,Biograph mCT,HiSeq2000,Illumina_HumanOmni1-Quadv1.0,Illumina_Omni5M,Illumina MouseWG-6 v2.0 expression beadchip,IlluminaNovaseq6000,IlluminaWholeGenomeDASL,Infinium Global Diversity Array-8,Illumina_Infinium-HumanMethylation450-BeadChip,IlluminaInfiniumGSAMD-24v2-0,IlluminaMethylationEPIC,PacBioRSII,IlluminaHumanMethylation450,IlluminaHumanHT-12_V3_0_R1,IlluminaHumanHap650Yv3_A,IlluminaHumanHap300,Illumina_Omni5-Quad,Biocrates p180,Illumina_Omni2pt5M,Illumina_Omni2.5-8_v1.3,Illumina_Omni2.5-8_v1.1,Illumina_Omni2.5-8,llumina Infinium General Screening Array 24-Kit v3.0,BGISEQ-500,Perlegen300Karray,AffymetrixU133Plus2,orbitrap,Xevo TQ-S,Agilent44Karray,NextSeq2000,NextSeq500,NanostringnCounter_MouseADPanel,NanostringnCounter,MiSeq,LTQOrbitrapXL,InfiniumPsychArrayBeadChip,Infinium Omni2.5Exome-8 v1.5,Infinium Omni2.5Exome-8 v1.4,Infinium Omni2.5Exome-8 v1.3,Infinium Omni2.5Exome-8 v1.1,Infinium HumanOmniExpressExome,OrbiTrap Fusion,Orbitrap Fusion Lumos,Olink Target 96,triple quadrupole,AffymetrixU133AB,Affymetrix Human Gene 1.0 ST Array,PacBio Sequel II,Xevo G2 QTOF,PsychChip,Affy6.0,Affy5.0,Illumina NovaSeq 6000,Q Exactive HF,Q Exactive,time-of-flight,Simoa HD-1 Analyzer,Signa Premier AIR 3T,IlluminaMiSeq,SequenomMultiplex,quadrupole time-of-flight,Q Exactive Plus | False | Sage Bionetworks | NGS | |
library_prep | The general strategy by which the library was prepared | STRING | lncRNAenrichment,SureCell,totalRNA,MULTIseq,multiome,miRNAenrichment,methylSeq,proximity ligation,EndItDNAEndRepairKit,STARRSeq,DNALibraryConstruction,Chromium Single Cell 3',cellHashing,amplicon,polyAselection,SPLITseq,rRNAdepletion,KapaHyperPrep,PCRfree | False | Sage Bionetworks | NGS | |
library_preparation_method | Method by which library was prepared | STRING | Drop-Seq,sac-seq,NexteraXT,Smart-seq1,10x,Omni-ATAC,Accel-NGS Methyl-Seq,CEL-seq,NEBNext,Smart-seq2,Smart-seq4,SMRTbell,TruSeq,Ultralow Methyl-Seq,Accel-NGS 2S Plus | False | Sage Bionetworks | Experimental_Data | |
library_type | The type of library, in assays where samples are barcoded or hashed for multiplexing or each sample has multiple libraries amplified separately before pooled sequencing. | STRING | ADT,plasmid DNA,HTO,CMO,LMO,cDNA,polyA enriched,ribozero depletion,globin depletion | False | NGS | ||
is_stranded | Whether or not the library is stranded | STRING | False,True | False | NGS | ||
read_strand_origin | The strand from which the read originates in a strand-specific protocol | STRING | forward,reverse | False | NGS | ||
run_type | The sequencing read types | STRING | singleEnd,pairedEnd | False | NGS | ||
reference_set | A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data. | STRING | GRCh37,GRCm38,MMUL1.0,HRC,1000 Genomes phase 3,GRCh38,dmel_r6.06 | False | NGS | ||
sample_status | Conditions under which sample is kept | STRING | Frozen,Paxgene,Formalin-fixed,Fresh | False | NGS | ||
analysis_type | Type of analysis | STRING | differential expression,eQTL | False | NGS | ||
nucleic_acid_source | STRING | bulk cell,bulk nuclei,single cell,single nucleus | True | NGS | |||
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 | STRING | fastq,count matrix,bam,csv,xlsx,txt,pdf,tsv | False | File_Annotations | ||
data_subtype | Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata. | STRING | raw,aligned,processed,normalized,aggregated | False | NGS | ||
data_type | Types of input/output data in bioinformatics pipelines | STRING | genomicVariants,geneExpression | True | Sage Bionetworks | NGS | |
sample_tissue_type | Tissue type used in sample | STRING | LP,EPI,both LP and EPI,blood,organoid | True | Biospecimen | ||
genomic_sex | The predicition of sex based on expression of genes | STRING | Male,Female | False | NGS | ||
library_id | Library ID as provided by the lab | STRING | False | NGS | |||
library_version | The version of the library. For example, rnaSeq 10x library version | STRING | False | NGS | |||
read_length | The length of the read | NUM | False | NGS | |||
analysis_thresholds | The minimum counts-per-million (CPM) threshold | NUM | False | NGS | |||
alignment_information | Alignment information | STRING | False | NGS | |||
vendor | Information about vendor (novagene) processes | STRING | False | NGS | |||
sample_barcode | The nucleotide sequence of the sample barcode used to identify cells from a single sample in cell hashing or multiplexing assays. | STRING | False | NGS | |||
RIN | RNA Integrity Number | NUM | False | Experimental_Data | |||
rna_batch | Batch in which RNA sample was isolated | STRING | False | Experimental_Data | |||
rna_isolation_kit | The technology used to isolate the RNA | STRING | False | Experimental_Data | |||
library_batch | Batch library was prepared in | STRING | False | NGS | |||
total_reads | Total number of raw sequencing reads from a library | NUM | False | NGS | |||
valid_barcode_reads | Fraction of reads with cell barcodes that match the whitelist | NUM | False | NGS | |||
number_cells | Number of cells or nuclei sequenced | NUM | False | NGS | |||
median_genes | The median number of genes detected (with nonzero UMI counts) across all cell-associated barcodes | NUM | False | NGS | |||
unique_genes | The number of unique genes | NUM | False | NGS | |||
mapped_reads | Mapped reads refer to those reads from the sequenced sample that align directly to a single region (set of loci) on the reference genome. | NUM | False | NGS | |||
rRNA_rate | The percentage of rRNA in a cell | NUM | False | NGS | |||
kit_number | Kit serial number | STRING | True | NGS | |||
DV200 | A method to determine the quality of RNA obtained from a sample. DV200 evaluates the percentage of fragments of greater than 200 nucleotides. | NUM | False | Experimental_Data | |||
duplication_rate | The duplication rate is the fraction of mapped reads where any 2 reads share the same 5_ and 3_ coordinates. | NUM | False | NGS | |||
median_umis | The median number of total Unique Molecular Identifier (UMI) counts across all cell-associated barcodes | STRING | False | NGS | |||
ratio_mitochondria | Percent mitochondria per cell | STRING | False | NGS | |||
individual_id | individual identifier | STRING | True | https://ncithesaurus.nci.nih.gov/ncitbrowser/ConceptReport.jsp?dictionary=NCI_Thesaurus&version=21.09d&code=C69256&ns=ncit | Clinical | ||
sample_id | sample identifier | True | |||||
Component | Category of metadata; provide the same one for all items/rows. | True | https://w3id.org/biolink/vocab/category |