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Bulk_ Rnaseq_Assay_Template

VEOIBD Bulk 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
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
sequencing_batch Batch library was sequenced 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
ratio260over230 Ratio of absorbance at 230 nm and 260 nm. Measures protein or other contaminants. Range up to approximately 2.2. NUM False Experimental_Data
ratio260over280 Measure of DNA vs. RNA purity. Range up to approximately 2.0. NUM False Experimental_Data
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
total_unmapped_reads The total number of unmapped reads from the sequenced sample to a single region (set of loci) on the reference genome. 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
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