Infinium Methylation Screening Array Manifest Column Headings
This article provides detailed descriptions of the column headings in the Infinium Methylation Screening (MSA) Array Manifest File (CSV). The associated product files can be accessed from the Infinium Methylation Screening Array Product Files page. The sections below describe each manifest column heading and the corresponding information provided to support data analysis, annotation, and interpretation.
IlmnID
Unique identifier extended with the following design strand designations
Illumina strand (T/B)
Assay Strand (C / O)
Infinium Design Type (1/2)
Rep_Num
Name
Unique identifier from the Illumina CG database
AddressA_ID
For Infinium I beadtypes, this is the Address ID for the probe specific for the A allele
For Infinium II beadtypes, this is the Address ID for the probe used for both A and B alleles (in this case AddressB_ID and AlleleB_ProbeSeq columns will be empty)
AlleleA_ProbeSeq
The sequence of the probe identified in the AddressA_ID column
AddressB_ID
For Infinium I beadtypes, this is the Address ID for the probe specific for the B allele
AlleleB_ProbeSeq
For Infinium I beadtypes, the sequence of the probe identified in the AddressB_ID column
Next_Base
For Infinium I probes, the nucleotide immediately following the CpG. Blank for Infinium II
Color_Channel
For Infinium I probes, the color channel of the Next_Base signal (Red/Green)
col
Color_Channel: For Infinium I probes the color channel of the Next_Base signal (R/G). Used for Bioconductor methylation array analysis software tools
Probe_Type
Probe type
cg=CpG
rs=dbSNP rsID
ch=Cp
Strand_FR
The Forward (F) or Reverse (R) designation of the Design Strand. F is equal to reference + strand
Strand_TB
The Illumina Top (T) or Bottom (B) designation of the Design strand
Strand_CO
The assay Converted (C) or Opposite (O) designation of the Design strand
Infinium_Design
Infinium Design (1) - 2 probes or (2) - 1 probe. Used for Bioconductor methylation array analysis software tools
Infinium_Design_Type
Infinium I (2 probes/locus) or Infinium II (1 probe/locus)
Rep_Num
Reflects the replicate number if the Name has replicate designs
CHR
Chromosome containing the CpG (GRCh38)
MAPINFO
Chromosomal coordinates of the CpG (GRCh38)
Species
Species which the assays were designed for (Homo sapiens)
Genome_Build
Genome Build referenced for this manifest
Source_Seq
The original genomic sequence used for probe design prior to bisulfite conversion
Forward_Sequence
Plus (+) strand sequence (5'-3') flanking the CG
Top_Sequence
Top strand sequence (5'-3') flanking the CG
UCSC_RefGene_Group
NCBI RefSeq Gene region
5UTR=5' untranslated region between the TSS and ATG start site
3UTR=3' untranslated region between stop codon and poly A signal
exon_#
TSS200=1-200 bp 5' the TSS
TSS1500=200-1500 bp 5' of the TSS
Intronic regions included
UCSC_RefGene_Name
NCBI RefSeq Gene Name: Target gene names from the RefSeq database. Multiple listings of the same gene name indicate splice variants
UCSC_RefGene_Accession
NCBI RefSeq Transcript ID: The RefSeq accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts
UCSC_CpG_Islands_Name
Chromosomal coordinates of the CpG Island from UCSC.
Relation_to_UCSC_CpG_Island
Island=within boundaries of a CpG Island
N_Shore=0-2kb 5' of Island
N_Shelf=2kb-4kb 5' of Island
S_Shore=0-2kb 3' of Island
S_Shelf=2kb-4kb 3' of Island
GencodeV41_Group
Gencode v41 Gene region
5UTR=5' untranslated region between the TSS and ATG start site
3UTR=3' untranslated region between stop codon and poly A signal
exon_#, TSS200=1-200 bp 5' the TSS
TS1500=200-1500 bp 5' of the TSS
Intronic regions included
GencodeV41_Name
Gencode v41 Gene Name: Target gene names from the RefSeq database. Multiple listings of the same gene name indicate splice variants
GencodeV41_Accession
Gencode v41 Transcript ID: The RefSeq accession numbers of the target transcripts. Accession numbers are in the same order as the target gene transcripts
Phantom5_Enhancers
Chromosomal coordinates from the FANTOM consortium of enhancer regions associated with FANTOM5 promoters
HMM_Island
Hidden Markov Model Islands. Chromosomal map coordinates of computationally predicted CpG islands
Regulatory_Feature_Name
Chromosomal map coordinates of the regulatory feature (informatically determined by the original ENCODE Consortium)
Regulatory_Feature_Group
Description of the regulatory feature referenced in Regulatory_Feature_Name as provided by the original ENCODE Consortium - Gene_Associated, Gene_Associated _Cell_type_specific, nonGene_Associated, Promoter_Associated_Cell_type_specific, Unclassified, Unclassified_Cell_type_specific
DNase_Hypersensitivity_NAME
Name of the DNase Hypersensitivity site as defined in ENCODE v5
Encode_CisReg_Site
Name and classification of the CisRegulatory Region as defined in ENCODE v5
Encode_CisReg_Site_Evid
Evidence for each CisReg Region/Classification based on 87 studies in ENCODE v5 based on AllData-Full classification
OpenChromatin_NAME
Classification of Open Chromatin sites based on 1600+ studies in ENCODE v5
OpenChromatin_Evidence_Count
Evidence for each Open Chromatin site classification based on 1600+ studies in ENCODE v5
EPICv2_Locus_Match
Locus Name (IlmnID) in Infinium MethylationEPICv2.0 Manifest
EPICv1_Locus_Match
Locus Name (IlmnID) in Infinium MethylationEPICv1.0 Manifest
Methyl450_Locus_Match
Locus Name (IlmnID) in Infinium Methylation450K Manifest
EPICv2_ProbeSeq_Match
Indicates if the AlleleA_ProbeSeq matches for EPIC v2
EPICv1_ProbeSeq_Match
Indicates if the AlleleA_ProbeSeq matches for EPIC v1
Methyl450_ProbeSeq_Match
Indicates if the AlleleA_ProbeSeq matches for Methylation450K
SNP_ID
rsIDs of SNPs located in the probe. Multiple listings of SNP rsIDs are allowed. dbSNP v155 used as reference
SNP_DISTANCE
Distance of SNPs from query base of the probe. Multiple listings of the distance values are associated with rsid. dbSNP v155 used as reference
SNP_MinorAlleleFrequency
Minor allele frequency of SNPs. Multiple listings of the minor allele frequencies are associated with rsid. dbSNP v155 used as reference
CHR_GRCh37
Chromosome containing the CpG (GRCh37)
MAPINFO_GRCh37
Chromosomal coordinates of the CpG (GRCh37)
References:
Additional information on the naming convention and logic used to generate IlmnIDs can be found in the following articles:* Description of suffixes in the cg probes ID in Infinium MethylationEPIC v2.0
Additional references:
For any feedback or questions regarding this article (Illumina Knowledge Article #10058), contact Illumina Technical Support techsupport@illumina.com.
Last updated
Was this helpful?