NDAABCDCCFOAINIAAADAAMP SCZHEALNBBPEC

Data Structure

SNP Array

Version 011086 Shared Subjects
Short Name: snp_array01
Data Type: Genomics
Categories: Omics

Metadata information about single nucleotide polymorphism (SNP) array experiment/project. SNP array is a type of DNA microarray containing designed probes harboring SNP positions. It is used to detect polymorphisms within a population.

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Definition
Submission Template

A Collection's submission must not be cumulative.

41 Elements

Name
Type
Required
Description
Value Range
Notes
subjectkeyGUIDRequiredThe NDAR Global Unique Identifier (GUID) for research subjectNDAR*
src_subject_idStringRequiredSubject ID how it's defined in lab/project
interview_dateDateRequiredDate on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_ageIntegerRequiredAge in months at the time of the interview/test/sampling/imaging.0::1440Age is rounded to chronological month. If the research participant is 15-days-old at time of interview, the appropriate value would be 0 months. If the participant is 16-days-old, the value would be 1 month.
sexStringRequiredSex of subject at birthM;F; O; NRM = Male; F = Female; O=Other; NR = Not reported
experiment_idIntegerRequiredID for the Experiment/settings/run
cellidStringRecommendedUnique identifier of cells
samplesubtypeIntegerRecommendedSubtype of sample, whether it is cells, nuclei, or bulk1::31=Cell; 2=Nucleus; 3=Bulk
libraryidStringRecommendedLibrary ID as provided by the lab
gen_softwareStringRecommendedName of the software used on sequencing platform
softwareversionStringRecommendedVersion number of the software used
referencesetIntegerRecommendedA set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data1::5; -991=1000 Genomes phase 3; 2=GRCh38; 3=GRCh37; 4=MMUL1.0; 5=HRC; -99=Other
otherreferencesetStringRecommendedA set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data
librarybatchStringRecommendedBatch library was prepared in
sequencingbatchStringRecommendedBatch library was sequenced in
libraryselectionIntegerRecommendedThe general strategy by which the library was prepared1::37; -88; -991=Random; 2=PCR Random PCR; 3=RT-PCR; 4=HMPR; 5=MF; 6=repeat fractionation; 7=size fractionation; 8=MSLL; 9=cDNA; 10=cDNA random priming; 11=cDNA oligo-dT; 12=PolyA; 13=Oligo-dT; 14=Inverse rRNA; 15=ChIP; 16=MNase; 17=DNase; 18=Hybrid selection; 19=Reduced representation; 20=Restriction digest; 21=5-methylcytidine antibody; 22=MBD2 protein methyl-CpG binding domain; 23=CAGE; 24=RACE; 25=MDA; 26=padlock probes capture method; 27=cell hashing; 28=DHA library construction; 29=EndItDNAEndRepairKit; 30=KapaHyperPrep; 31=IncRNAenrichment; 32=MULTIseq; 33=PCR-free; 34=rRNA depletion; 35=SPLITseq; 36=STARRseq; 37=SureCell; -99=Other; -88=Unspecified
libraryconstructionprotocolIntegerRecommendedMethod used to construct the sequence library1::31; -991=SMART-seq; 2=SMART-seq2; 3=SMART-seq3; 4=SMART-seq4; 5=STRT-seq; 6=STRT-seq-C1; 7=STRT-seq-2i; 8=Quartz-seq; 9=Quartz-seq2; 10=CEL-seq; 11=CEL-seq2; 12=10x Chromium Single Cell 3' V3 FeatureBarcoding; 13=10x Chromium Single Cell 3' V2 and V3 GE; 14=10x Chromium Single Cell 3' V1 GE; 15=10x Chromium Single Cell 5' VDJ; 16=10x Chromium Single Cell 5' GE; 17=SureCell 3' WTA for ddSEQ; 18=MARS-seq / MARS-seq2.0; SCRB-seq / mcSCRB-seq; 18=Drop-seq / Seq-Well; 19=scifi-RNA-seq; 20=Microwell-seq; 21=BD Rhapsody; 22=sci-RNA-seq3; 23=sci-RNA-seq; 24=Seq-Well S3; 25=Tang 2009; 26=SPLiT-seq; 27=inDrop; 28=NEBNext; 29=NexteraXT; 30=Omni-ATAC; 31=10x Visium Gene Expression protocol; -99=Other
otherlibraryconstructprotocolStringRecommendedOther type of library construction protocol not listed
librarysourceIntegerRecommendedThe type of source material that is being sequenced1; 2; -991=Genomic; 2=Genomic single cell; -99=Other
otherlibrarysourceStringRecommendedOther library source not listed
readlengthFloatRecommendedThe length of the read
librarylayoutIntegerRecommendedIf the library is paired-end or single-end1; 21=Single; 2=Paired-end
totalreadsIntegerRecommendedTotal number of sequencing reads from a library
numbercellsIntegerRecommendedNumber of cells or nuclei sequenced
dnabatchStringRecommendedDNA isolation batch
gen_gqnFloatRecommendedIllumina gDNA quality score
ratio260over230FloatRecommendedRatio of absorbance at 230 nm and 260 nm. Measures protein or other contaminants. Range up to approximately 2.2
ratio260over280FloatRecommendedMeasure of DNA vs. RNA purity. Range up to approximately 2.0
arraybatchStringRecommendedThe hybridization batch the sample was in
data_file1FileRecommendedData file 1
data_file1_typeStringRecommendedtype of data file 1
genotyping_chip_typeStringRecommendedChip type used for genotyping
rat230FloatRecommendedRatio of absorbance at 260nm and 230nm
rat280FloatRecommendedRatio of absorbance at 260nm and 280nm
sample_id_biorepositoryStringRecommendedBiorepository Sample ID
studyStringRecommendedStudy; The code for each individual study
total_rna_dnaFloatRecommendedTotal RNA (micrograms) OR Total DNA (micrograms)
psych_enc_excludeIntegerRecommendedSubject excluded from study0;1;9990=No; 1=Yes; 999=Missing
psych_enc_exclude_reasonStringRecommendedReason subject was excluded from study
platformStringRecommendedName of particular experiment platform
assayIntegerRecommendedThe technology used to generate the data in this file0::15; 9990=ATACSeq; 1=CUT(and)Tag; 2=ChIPSeq; 3=GO-CaRT; 4=HI-C; 5=RNA-seq; 6=TMT quantitation; 7=bisulfiteSeq; 8=errBisulfiteSeq; 9=label free mass spectrometry; 10=methylationArray; 11=mirnaSeq; 12=oxBS-Seq; 13=scrnaSeq; 14=snpArray; 15=wholeGenomeSeq; 999=Missing