Methyl-seq Standard Analysis Demo Data

Publications

Cheng Y, Vechtova P, Fussy Z, Sterba J, Linhartová Z, Rodina M, Tučková V, Gela D, Samarin AM, Lebeda I, Xin M, Zhang S, Rahi D, Linhart O. Changes in Phenotypes and DNA Methylation of In Vitro Aging Sperm in Common Carp Cyprinus carpio. Int J Mol Sci. 2021 May 31;22(11):5925. doi: 10.3390/ijms22115925. PMID: 34073009; PMCID: PMC8198300.

One μg of total DNA of each sample was sent for WGBS to Admera Health Biopharma Services.

Brick K, Thibault-Sennett S, Smagulova F, Lam KG, Pu Y, Pratto F, Camerini-Otero RD, Petukhova GV. Extensive sex differences at the initiation of genetic recombination. Nature. 2018 Sep;561(7723):338-342. doi: 10.1038/s41586-018-0492-5. Epub 2018 Sep 5. PMID: 30185906; PMCID: PMC6364566.

Sequencing was performed on an Illumina HiSeq 2500 at the NIDDK genomics core and on an Illumina HiSeq X Ten by Admera Health.

Rodriguez-Casariego JA, Cunning R, Baker AC, Eirin-Lopez JM. Symbiont shuffling induces differential DNA methylation responses to thermal stress in the coral Montastraea cavernosa. Mol Ecol. 2022 Jan;31(2):588-602. doi: 10.1111/mec.16246. Epub 2021 Nov 5. PMID: 34689363.

Libraries were barcoded and shipped for pooling and sequencing at Admera Health Biopharma Services, generating 150 bp paired-end reads on two lanes of a HiSeq-X sequencer.

Kelly Gomez-Campo, Robersy Sanchez, M. Martinez-Rugerio, et al. Phenotypic plasticity in coral skeletal features: Molecular signatures from DNA methylation and transcriptional interaction networks. Authorea. May 16, 2023. DOI: 10.22541/au.168423509.93827399/v1

gDNA concentration was quantified at 0.5-1.5 μg (Qubit® dsDNA BR Assay Kit on a Qubit® 2.0. Fluorometer) and sent for Whole Genome Bisulfite Sequencing (WGBS) at Admera Health (New Jersey, USA).

Senapati P, Miyano M, Sayaman RW, Basam M, Leung A, LaBarge MA, Schones DE. Loss of epigenetic suppression epithelial cells. Genome Res. 2023 Jul 18:gr.277511.122. doi: 10.1101/gr.277511.122. Epub ahead of print. PMID: 37463750.

WGBS-seq was performed at Admera Health Biopharma Services.

Parijat Senapati, Masaru Miyano, Rosalyn W. Sayaman, Mudaser Basam, Candi Trac, Amy Leung, View ORCID ProfileMark A. LaBarge, View ORCID ProfileDustin E. Schones. Normal mammary epithelia accumulate DNA methylation changes with age that are consistent with breast cancer methylomes. doi: https://doi.org/10.1101/2020.06.26.170043

Whole-genome bisulfite sequencing (WGBS-seq) was performed at Admera Health Biopharma Services.

Domin A, Zabek T, Kwiatkowska A, Szmatola T, Deregowska A, Lewinska A, Mazur A, Wnuk M. The Identification of a Novel Fucosidosis-Associated FUCA1 Mutation: A Case of a 5-Year-Old Polish Girl with Two Additional Rare Chromosomal Aberrations and Affected DNA Methylation Patterns. Genes (Basel). 2021 Jan 8;12(1):74. doi: 10.3390/genes12010074. PMID: 33435586; PMCID: PMC7827884.

Reduced representation bisulfite sequencing (RRBS) libraries were pooled in groups of six and sequenced in a 75 bp single-end read on the NextSeq 550 system (Illumina) (Admera Health, La Jolla, CA, USA).

Kain, B.N., Tran, B.T., Luna, P.N., Cao, R., Le, D.T., Florez, M., Maneix, L., Toups, J., Morales-Mantilla, D., Koh, S., Han, H., Jaksik, R., Huang, Y., Catic, A., Shaw, C.A., King, K.Y., Hematopoietic stem and progenitor cells confer cross-protective trained immunity in mouse models, ISCIENCE (2023), doi: https://doi.org/10.1016/j.isci.2023.107596.

Samples were sequenced at Admera Health using an Illumina HiSeq 2x150 at sequencing depth of 40 million reads