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| Status |
Public on Jul 18, 2019 |
| Title |
control rep17 |
| Sample type |
SRA |
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| Source name |
endometrial tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: endometrial tissue
disease state: control
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Endometrial tissue was lysed using Qiagen ATL buffer supplemented with Proteinase K at 55C overnight. DNA was extracted using the Qiagen DNAeasy Blood and Tissue kit
To produce methyl enriched DNA fragments, sonicated DNA was subjected to the Methylated-CpG Island Recovery Assay (MethylCollector Ultra – Active Motif). Enriched methyl DNA was then subjected to library construction using the NEBNext DNA library prep kit for Illumina (New England Biolabs)
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| Library strategy |
MBD-Seq |
| Library source |
genomic |
| Library selection |
MBD2 protein methyl-CpG binding domain |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
N_0060
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| Data processing |
checked the quality of the data using FastQC
remove reads with low‐quality bases, adapter sequences, and other contaminating sequences using Cutadapt
Bowtie2 was used to build the index of reference genome
Each sample’s reads were aligned against the reference genome hg38 using Bowtie2
we used Samtools and Picard for sorting and removing duplicate reads, respectively
we segmented the genome sequence into 1,000 bases tiling windows and then recorded the number of reads that are mapped to each methylated regions. Read counts are the number of aligned reads that uniquely map to the hg38 reference genome. Several R packages (MEDIPS, BSgenome, BSgenome.Hsapiens.UCSC.hg38)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file includes the raw read counts of each 1,000 bases tiling windows for all samples
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| Submission date |
Jul 09, 2019 |
| Last update date |
Jul 18, 2019 |
| Contact name |
Susan Nagel |
| E-mail(s) |
nagels@health.missouri.edu
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| Organization name |
University of Missouri
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| Street address |
One Hospital Drive
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| City |
Columbia |
| State/province |
Missouri |
| ZIP/Postal code |
65201 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE134052 |
Machine Learning Classifiers for Endometriosis Using Transcriptomics and Methylomics Data [Methylomics] |
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| Relations |
| BioSample |
SAMN12238972 |
| SRA |
SRX6422827 |
| 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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