GEO DataSets

(Submitter supplied) Background: Ultra-Conserved-Non-coding Elements (UCNEs) are genomic sequences that exhibit >95% sequence identity between human, mammals, birds, reptiles and fishes. Recent findings reported their functional role in cancer. Aim of this study was to evaluate their DNA methylation modifications in squamous cell carcinoma (SCC) from different mammal species Methods: Fifty SCC from 26 humans, 17 cats, 3 dogs, 1 horse, 1 bovine, 1 badger and 1 porcupine were investigated. more...

Organism:

Felis catus; Bos taurus; Homo sapiens; Canis lupus familiaris; Equus caballus; Meles meles; Hystrix cristata

Type:

Methylation profiling by high throughput sequencing

7 related Platforms

120 Samples

Download data: XLSX

(Submitter supplied) Genome wide DNA methylation profiling of normal and adjacent OSCC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 4,50,000 CpGs in tissue samples. Total 21 samples were taken including 10 paired and 1 unpaired tissues. 6 were HPV Positive and 5 were HPV negative.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

21 Samples

Download data: IDAT

(Submitter supplied) Objectives: Earlier studies involving a priori gene selection have identified promoter regions deregulated by DNA methylation changes in oral squamous cell cancers (OSCCs) and precancers. Interrogation of global DNA methylation patterns for such specimens has not been reported, though such analyses are needed to uncover novel molecular factors driving disease. Materials and Methods: We evaluated global DNA methylation patterns for 30 biopsies obtained from 10 patients undergoing surgical removal of an OSCC or carcinoma in situ (CIS). more...

Organism:

Homo sapiens

Type:

Methylation profiling by array; Expression profiling by array

Platforms:

GPL8490 GPL6480

60 Samples

Download data: TXT

(Submitter supplied) Genome wide DNA methylation profiling of three normal (N) and eight ulcerative colitis (UC) samples as well as one human colon cancer cell (HCT116) . The Illumina Infinium 450k Human DNA methylation platform was used to obtain DNA methylation profiles across approximately 480,000 CpGs.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

12 Samples

Download data: IDAT, TXT

(Submitter supplied) Methylated genomic fragments from tumor and matching normal DNA were enriched with the methylated-CpG island recovery assay (MIRA); amplified, labeled and hybridized on Agilent CpG island tiling oligo arrays. Samples from tumor were labeled with Cy5 while the matching normal were labeled with Cy3 so that methylation differences can be detected. Keywords: Cancer

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL4126

5 Samples

Download data: GPR

(Submitter supplied) DNA methylation in esophageal squamous cell carcinoma (ESCC)

Organism:

Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL13534

10 Samples

Download data: CSV

(Submitter supplied) Comprehensive DNA methylation analysis in clinical samples of lung squamous cell carcinoma with or without tidiopathic pulmonary fibrosis. Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across 485,577 CpG sites. Samples included 20 lung squamous cell carcinoma with or without tidiopathic pulmonary fibrosis and 13 surrounding lung samples.

Organism:

Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL13534

33 Samples

Download data: TXT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues from horses We generated DNA methylation data from n=333 horse tissue samples representing tissues. Blood samples were collected via venipuncture into EDTA tubes from across 24 different horse breeds (buffy coat). The other tissues were collected at necropsy. The tissue atlas was generated from two Thoroughbred mares as part of the FAANG initiative 37, with the following tissues profiled: adipose (gluteal), adrenal cortex, blood (PBMCs; only n=1 mare), cartilage (only n=1 mare), cecum, cerebellum (2 samples each from lateral hemisphere and vermis), frontal cortex, duodenum, fibroblast, heart (2 samples each from the right atrium, left atrium, right ventricle, left ventricle), hypothalamus, ileum, jejunum, keratinocyte, kidney (kidney cortex and medulla), lamina, larynx (i.e. more...

Organism:

Homo sapiens; Equus caballus; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

333 Samples

Download data: IDAT, TXT

(Submitter supplied) Illumina Infinium HumanMethylation850 BeadChip (also known as Illumina EPIC array, GPL23976) was used to generate DNA methylation data from synthetic DNA from 3 species. The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. more...

Organism:

Mus musculus; Rattus norvegicus; Homo sapiens

Type:

Methylation profiling by array

Platform:

GPL23976

28 Samples

Download data: IDAT, TXT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from synthetic DNA from 3 species. The DNA samples from each species were enzymatically manipulated so that they would exhibit 0%, 25%, 50%, 75% and 100% percent methylation at each CpG location, respectively. The variable “ProportionMethylated” (with ordinal values 0, 0.25, 0.5, 0.75, 1) can be interpreted as a benchmark for each CpG that maps to the respective genome. more...

Organism:

Homo sapiens; Mus musculus; Rattus norvegicus

Type:

Methylation profiling by array

Platform:

GPL28271

45 Samples

Download data: IDAT, TXT

(Submitter supplied) An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from several tissues in several bat species. Tissues: skin (wing punches), liver, brain, skeletal muscle.

Organism:

Rousettus aegyptiacus; Desmodus rotundus; Rattus norvegicus; Myotis lucifugus; Rhynchonycteris naso; Pteropus poliocephalus; Pteropus hypomelanus; Phyllostomus hastatus; Eptesicus fuscus; Nyctalus noctula; Cynopterus brachyotis; Rhinolophus ferrumequinum; Myotis vivesi; Tadarida brasiliensis; Carollia perspicillata; Eidolon helvum; Pteropus rodricensis; Myotis brandtii; Pteropus giganteus; Pteropus pumilus; Leptonycteris yerbabuenae; Artibeus jamaicensis; Antrozous pallidus; Homo sapiens; Mus musculus; Molossus molossus; Nycticeius humeralis; Myotis myotis; Saccopteryx bilineata; Phyllostomus discolor; Pteropus vampyrus

Type:

Methylation profiling by array

Platform:

GPL28271

908 Samples

Download data: DOCX, IDAT, TXT

(Submitter supplied) We generated sequencing data for 104 dogs using targeted-bisulfite sequencing with targets selected to the human 450K methylation array. Using these data, we identify a conserved methylation signature that can be used to quantitatively translate dog years to human years and also extends to mice.

Organism:

Canis lupus familiaris

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL24229

109 Samples

Download data: TXT