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Bisulfite Sequencing

0 Shared Subjects

Metadata information about Bisulfite sequencing (Bisulfite-seq) experiment/project. Bisulfite sequencing is the use of bisulfite treatment of DNA before sequencing to determine the pattern of methylation.
Omics
Omics
05/23/2022
bisulfite_seq01
03/13/2024
View Change History
01
Definition
Submission Template
Query Element Name Data Type Size Required Description Value Range Notes Aliases
subjectkey GUID Required The NDAR Global Unique Identifier (GUID) for research subject NDAR*
src_subject_id String 20 Required Subject ID how it's defined in lab/project
interview_date Date Required Date on which the interview/genetic test/sampling/imaging/biospecimen was completed. MM/DD/YYYY
interview_age Integer Required Age in months at the time of the interview/test/sampling/imaging. 0::1440 Age 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.
sex String 20 Required Sex of subject at birth M;F; O; NR M = Male; F = Female; O=Other; NR = Not reported
experiment_id Integer Required ID for the Experiment/settings/run
cellid String 4,000 Recommended Unique identifier of cells
samplesubtype Integer Recommended Subtype of sample, whether it is cells, nuclei, or bulk 1::3 1=Cell; 2=Nucleus; 3=Bulk
libraryid String 4,000 Recommended Library ID as provided by the lab
gen_software String 4,000 Recommended Name of the software used on sequencing platform
softwareversion String 4,000 Recommended Version number of the software used
referenceset Integer Recommended A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data 1::5; -99 1=1000 Genomes phase 3; 2=GRCh38; 3=GRCh37; 4=MMUL1.0; 5=HRC; -99=Other
otherreferenceset String 4,000 Recommended A set of references (e.g., canonical assembled contigs) which defines a common coordinate space for comparing reference-aligned experimental data
librarybatch String 4,000 Recommended Batch library was prepared in
sequencingbatch String 4,000 Recommended Batch library was sequenced in
libraryselection Integer Recommended The general strategy by which the library was prepared 1::37; -88; -99 1=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
libraryconstructionprotocol Integer Recommended Method used to construct the sequence library 1::30; -99 1=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; -99=Other
otherlibraryconstructprotocol String 4,000 Recommended Other type of library construction protocol not listed otherlibraryconstructionprotocol
librarysource Integer Recommended The type of source material that is being sequenced 1; 2; -99 1=Genomic; 2=Genomic single cell; -99=Other
otherlibrarysource String 4,000 Recommended Other library source not listed
readlength Float Recommended The length of the read
librarylayout Integer Recommended If the library is paired-end or single-end 1; 2 1=Single; 2=Paired-end
totalreads Integer Recommended Total number of sequencing reads from a library
numbercells Integer Recommended Number of cells or nuclei sequenced
readstrandorigin Integer Recommended The strand from which the read originates in a strand-specific protocol 1::4; 999 1=Forward; 2=Reverse; 3=Unstranded; 4=First-strand; 999=Missing
isstranded Integer Recommended Whether or not the library is stranded. 0; 1 0=No; 1=Yes
pcrcycles Integer Recommended Number of PCR cycles to amplify transposased DNA fragments
meancoverage Float Recommended Total number of bases covered by ATAC-seq reads/size of genome
directionalbsseqlibrary Integer Recommended Indicates whether or not the bisulfiteSeq library is directional 0; 1 0=No; 1=Yes
gdnaconc Float Recommended gDNA Concentration in ng
lambdadnaconc Float Recommended Lambda DNA spike-in concentration in ng
data_file1 File 255 Recommended Data file 1
data_file1_type String 300 Recommended type of data file 1
dnabatch String 4,000 Recommended DNA isolation batch
library_prep_batch String 255 Recommended Sequencing library batch
platform String 255 Recommended Name of particular experiment platform
sample_id_biorepository String 100 Recommended Biorepository Sample ID
assay Integer Recommended The technology used to generate the data in this file 0::15; 999 0=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
readlength_max Float Recommended The maximum length of the read
readlength_min Float Recommended The minimum length of the read
Data Structure

This page displays the data structure defined for the measure identified in the title and structure short name. The table below displays a list of data elements in this structure (also called variables) and the following information:

  • Element Name: This is the standard element name
  • Data Type: Which type of data this element is, e.g. String, Float, File location.
  • Size: If applicable, the character limit of this element
  • Required: This column displays whether the element is Required for valid submissions, Recommended for valid submissions, Conditional on other elements, or Optional
  • Description: A basic description
  • Value Range: Which values can appear validly in this element (case sensitive for strings)
  • Notes: Expanded description or notes on coding of values
  • Aliases: A list of currently supported Aliases (alternate element names)
  • For valid elements with shared data, on the far left is a Filter button you can use to view a summary of shared data for that element and apply a query filter to your Cart based on selected value ranges

At the top of this page you can also:

  • Use the search bar to filter the elements displayed. This will not filter on the Size of Required columns
  • Download a copy of this definition in CSV format
  • Download a blank CSV submission template prepopulated with the correct structure header rows ready to fill with subject records and upload

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