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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 04, 2020 |
| Title |
MCPR5TUCR (MCPR5) |
| Sample type |
SRA |
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| Source name |
oral mucosa
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| Organism |
Homo sapiens |
| Characteristics |
disease state: SCC
tissue: oral brush
age: 67
tnm: T4N0M0
cell type: Oral Squamous Cell Carcinoma
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| Treatment protocol |
Formali Fixed Paraffin Embedded Tissue or oral brushing specimens
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| Growth protocol |
none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
MasterPure DNA purification kit or QuickExtract FFPE DNA Extraction kit
Locus-specific amplicon libraries were generated with tagged primers in two steps: a first PCR amplification for target enrichment, and a second shorter amplification session (8 cycles) to allow the barcoding of the template-specific amplicons obtained from the first amplification step using the Nextera™ Index Kit (Illumina, San Diego, CA, USA)
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina MiSeq |
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| Data processing |
Reads were mapped by BWAmeth generating the .bam file which was processed by MethylDackel using hg38 for human samples, Felis_catus_9.0 for feline samples as a reference;
EPIC-TABSAT web-tool
Methylation Plotter Webtool
ClustVis webtool
EasyROC
Genome_build: hg38
Supplementary_files_format_and_content: Table 1: Clinical details of mammalian species other than human included in this study:
Supplementary_files_format_and_content: Table 2: genomic regions investigated in this study (reference genome: hg38; gene annotations were retrieved from UCNE database[2] and from Bajerano database[1]):
Supplementary_files_format_and_content: Table 3: Best and worst AUC values for all the seven UCNEs; the number indicates the position on the genome taking into account hg38 as a reference:
Supplementary_files_format_and_content: Table S1: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for each position and group of samples comparing all SCC from all the species together vs normal samples and feline stomatitis
Supplementary_files_format_and_content: Table S2: Summary Table comparing human normal donors vs SCC
Supplementary_files_format_and_content: Table S3: Summary Table with the mean, the standard deviation, the minimum, the maximum and p value of the Kruskal-Wallis test for feline SCC vs feline normal samples and feline stomatitis
Supplementary_files_format_and_content: TUCRDataFinalJuly2020: methylation level of each CpG for all cases
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| Submission date |
Sep 03, 2020 |
| Last update date |
Sep 04, 2020 |
| Contact name |
Luca Morandi |
| E-mail(s) |
luca.morandi2@unibo.it
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| Organization name |
University of Bologna
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| Department |
DIBINEM
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| Lab |
Neurogenetics, Pavillion I
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| Street address |
via Altura 3
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| City |
Bologna |
| ZIP/Postal code |
40139 |
| Country |
Italy |
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| Platform ID |
GPL15520 |
| Series (1) |
| GSE157436 |
An Evolutionary Cancer Epigenetic approach revealed DNA hypermethylation of Ultra-Conserved Non-coding Elements in squamous cell carcinoma of different mammalian species |
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| Relations |
| BioSample |
SAMN16053626 |
| SRA |
SRX9069591 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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