Infinium Mouse Methylation Beadchip manifest column headings

Infinium Mouse Methylation BeadChip product files are available on the Infinium Mouse Methylation BeadChip Support Resources page.

This article refers specifically to the Infinium Mouse Methylation Manifest File (CSV).

IlmnID: Unique identifier from the Illumina CG database with four added alphabetic and numeric characters to denote:

• Top or bottom strand (T/B) (Strand_TB)

• Converted or opposite strand (C/O) (Strand_CO)

• Infinium probe type (1/2) (Infinium_Design_Type)

• Number of syntheses for representation of the probe on the array (1,2,3,…,n) (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, the Address ID for the probe specific for the A allele, which is the unmethylated allele.

• For Infinium II bead types, 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.

Strand_TB: The Top (TOP or T) or Bottom (BOT or B) designation of the Design Strand using the Illumina standard designation for sequences harboring ambiguous SNPs. The T/B is part of the IlmnID as described above. 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 that 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 is part of the IlmnID as described above.

Infinium_Design_Type: Infinium I (two probes/locus) or Infinium II (one probe/locus). The Infinium probe type is part of 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 probes generated from the second and third syntheses would be denoted as “2” and “3”.

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 the Illumina technique for determining TOP/BOT strands for genotyping, using the CpG dinucleotide in question rather than the SNP variant.

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 & 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 [e-mail].

For any feedback or questions regarding this article (Illumina Knowledge Article #5894), contact Illumina Technical Support [e-mail].