Infinium Mouse Methylation Manifest Column Headings
This article provides detailed descriptions of the column headings included in the Infinium Mouse Methylation Manifest File (CSV). The associated product files can be accessed from the Infinium Mouse Methylation BeadChip Support Resources page. The sections below describe each manifest column heading and the corresponding information it provides to support data analysis, annotation, and interpretation.
IlmnID
Unique identifier from the Illumina CG database with four added alphabetic and numeric characters to denote:
Top or bottom strand (T/B) (s. Strand_TB)
Converted or opposite strand (C / O) (s. Strand_CO)
Infinium probe type (1/2) (s. Infinium_Design_Type)
Number of synthesis for representation of the probe on the array (1,2,3,…,n) (s. Rep_Num)
Example:cg00101675_BC21
Name
The locus target identifier (cg, ca, cc, ct, cl, rs) followed by an eight-digit code that relates to the probe sequence. If an eight-digit code has not yet been generated, standard genomic coordinates follow the locus target identifier.
AddressA_ID
For Infinium I bead types, this is the Address ID for the probe specific for the A allele, which is the unmethylated allele.
For Infinium II bead types, this is the Address ID for the probes used for both A and B alleles. In this case, AddressB_ID and AlleleB_ProbeSeq columns are empty.
AlleleA_ProbeSeq
The sequence of the probe identified in the AddressA_ID column.
AddressB_ID
For Infinium I bead types, the address ID for the probe specific for the B allele, which is the methylated allele.
AlleleB_ProbeSeq
For Infinium I bead types, 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.
Col
The intended color channel for the probes. Red and green are abbreviated to “R” and “G”, respectively.
Probe_Type
Either “ctl”, “cg”, “ch”, “mu”, “rp”, or “rs” to denote control, CpG, CHG, multi-unique, repetitive element, or SNP probes. Multi-unique probes are probes that map perfectly to multiple sites in the mouse reference genome outside of defined repetitive element regions.
Strand
The Forward (F) or Reverse (R) designation of the Design Strand.
*Note: In methylation manifest files, the Forward Strand = the genomic Plus (+) Strand and the Reverse Strand = the genomic Minus (-) Strand. In this context, Forward and Reverse ARE NOT EQUIVALENT to the Forward and Reverse Strand designations originating from reference genome build or as given in Infinium Genotyping manifests (s. DNA strand designations).
Strand_TB
The Top (TOP or T) or Bottom (BOT or B) designation of the Design Strand using the Illumina's standard designation for sequences harboring ambiguous SNPs. The T/B designation is incorporated into the IlmnID, as described above. For further details on TOP/BOT strand assignment and A/B allele nomenclature, refer to the bulletin Simple guidelines for identifying top/bottom (TOP/BOT) strand and A/B allele for further detail.
Strand_CO
The Converted (C) or Opposite (O) designation of the Design Strand which relates to whether the probe is designed to the strand that is originally converted by bisulfite or the opposite strand that arises after random primer amplification of DNA. The C / O designation is incorporated into the IlmnID, as described above.
Infinium_Design_Type
Infinium I (two probes/locus) or Infinium II (one probe/locus). The Infinium probe type is incorporated into the IlmnID as described above.
Rep_Num
This value depends on how many times a probe was synthesized for representation on the array. As seen in the IlmnID described above, if the probe was synthesized three separate times, the probe generated by the first synthesis would be denoted as “1”, while the probe generated from the second and third syntheses would be denoted as “2” and “3” respectively.
CHR
Chromosome containing the CpG (designation currently from build mm10).
MAPINFO
Chromosomal coordinates of the CpG (from build mm10).
Species
Name of the species for which a given probe was designed to target.
Genome_Build
Genome Build of the consensus mouse genome.
SourceSeq
The original, genomic sequence used for probe design after bisulfite conversion.
Forward_Sequence
Plus (+) strand sequence (5'-3') flanking the CG.
Top_Sequence
The sequence of the designated TOP strand using Illumina's technique for determining TOP/BOT strands for genotyping, but for the CpG dinucleotide in question rather than for a genetic SNP.
Genome_Build_NCBI
NCBI genome build ID for consensus mouse genome (GRCm38).
N_Shelf
Genomic coordinates of a CpG Island North Shelf, where the array has targeted a CpG within the shelf. The definition of a North Shelf is the region 4,000 to 2,000 base pairs upstream of a CpG Island start site.
N_Shore
Genomic coordinates of a CpG Island North Shore, where the array has targeted a CpG within the shore. The definition of a North Shore is the region 2,000 to 0 base pairs upstream of a CpG Island start site.
CpG_Island
Genomic coordinates of a CpG Island, where the array has targeted a CpG within the island. CpG Islands are regions greater than 200 base pairs in length with GC content of 50% or greater and have a ratio of > 0.6 for the observed number of CG dinucleotides to the expected number considering the total number of G and C bases in the genome segment.
CpG_Island_Chrom
Chromosome where the array has targeted a CpG within a CpG island on the chromosome.
CpG_Island_chromStart
Genome coordinate that denotes the start site of a CpG Island where the array has targeted a CpG within the island.
CpG_Island_chromEnd
Genome coordinate that denotes the stop site of a CpG Island where the array has targeted a CpG within the island.
CpG_Island_Length
Overall nucleotide length of the CpG Island in which the array has targeted a CpG within the island.
CpG_Island_cpgNum
The number of CpGs within a given CpG Island in which the array has targeted a CpG within the island.
CpG_Island_gcNum
The number of G and C bases within a CpG Island in which the array has targeted a CpG within the island.
CpG_Island_perCpg
The percent of CpG dinucleotides as compared to the total bases in a CpG island, where the array has targeted a CpG within the island.
CpG_Island_perGc
The percent of G and C bases within a given CpG island sequence, where the array has targeted a CpG within the island.
CpG_Island_obsExp
The ratio of observed to expected CpG dinucleotides within a CpG island in which the array has targeted a CpG within the island.
S_Shore
Genomic coordinates of a CpG Island South Shore, where the array has targeted a CpG within the shore. The definition of a South Shore is the region 0 to 2,000 base pairs downstream of the stop site of a CpG Island.
S_Shelf
Genomic coordinates of a CpG Island South Shelf, where the array has targeted a CpG within the shelf. The definition of a North Shelf is the region 2,000 to 4,000 base pairs downstream of the stop site of a CpG Island.
MFG_Change_Flagged
Indicates whether Illumina has detected changes in the functional performance of a specific probe resulting from a change in manufacturing, or if probes generated in different synthesis events function in an unanticipated manner during internal testing.
Listed as “False” to indicate that no change in functional performance has been detected due to a given manufacturing change (more common).
Listed as “True” to indicate if an effect to the functional performance has been detected after a manufacturing change.
For additional questions, contact Illumina Technical Support at techsupport@illumina.com.
For any feedback or questions regarding this article (Illumina Knowledge Article #5894), contact Illumina Technical Support techsupport@illumina.com.
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