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| Status |
Public on Jan 23, 2018 |
| Title |
RRBS on normal crypts, patient #178 |
| Sample type |
SRA |
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| Source name |
Colon
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Healthy individual
tissue: normal colonic crypt
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| Growth protocol |
CRYPTS: All ACF subjects included in this study were enrolled in an ongoing clinical study at John Dempsey Hospital (UConn Health). All patients who met the Amsterdam criteria for familial adenomatous polyposis (FAP) or hereditary non-polyposis CRC (HNPCC) were excluded from this study. In order to control for the effects of age and smoking on DNA methylation, all selected subjects were non-smokers between the ages of 50 and 65. 10 ACF were biopsied from the distal colons of individual subjects. ACF were identified and biopsied during high-definition, magnifying chromoendoscopy using indigo carmine dye-spray. For each subject, a sample of normal-appearing mucosa was also obtained from the distal colon. Biopsies were immediately embedded in OCT freezing medium (Neg 50, ThermoFisher Scientific), flash-frozen, and stored at -80C. Frozen tissues were sectioned onto polyethylene naphthalate (PEN, ThermoFisher Scientific) membrane slides using a Leica CM1900 Cryostat. Frozen sections were stained with hematoxylin and eosin (H&E) and routine histologic analyses were performed. All biopsies collected from ACF subjects were histologically confirmed by a board-certified human gastrointestinal pathologist blinded.
CRC: Ten Stage II-IV CRCs resected from the distal colons of individual subjects were obtained from the City of Hope and University of Connecticut Health frozen tumor banks. In addition, 10 histologically-confirmed matched normal samples, collected from the margins on either side of the resected tumor, were obtained. Tissue sections were stained with H&E and reviewed by a board-certified pathologist to confirm the presence and histopathology of the lesions. This study was conducted with the written, informed consent of each subject, as well as Institutional Review Board approval from both the University of Connecticut Health and City of Hope (IRB Protocols IE-10-068OSJ-3 and 97134, respectively).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
CRYPTS: Laser Capture Microdissection of ACF and matched normal biopsies: an ArcturusXT Laser Capture Microdissection system was used to isolate a minimum of 1 mm2 of tissue (~10.000 cells) from 12 μm-thick frozen serial sections.
CRC: RNA was isolated from laser-captured ACF samples using the Arcturus PicoPure Frozen RNA Isolation Kit (ThermoFisher) according to the manufacturers' instructions. RNA was isolated from cancer patient frozen tissues using the mirVana miRNA Isolation Kit (Ambion) according to the manufacturers' instructions
RRBS: Briefly, purified DNA was digested by overnight incubation with MspI at 37°C. Following restriction digest, DNA fragments were subjected to end repair and A-tailing, followed by linker ligation. Bisulfite conversion was done using the EZ DNA Methylation-Gold Kit (Zymo Research) according to the manufacturer’s instructions
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Data were aligned to hg19 genome using Bismark v0.7.4
Reads were imported into R, extended to 200bp and coverage of each base was calculated using customized R scripts to generate the bedGragh files.
Genome_build: hg19
Supplementary_files_format_and_content: bedgraph with methylation levels
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| Submission date |
Mar 03, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiwei Wu |
| E-mail(s) |
[email protected]
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| Organization name |
City of Hope National Medical Center
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| Department |
Computational and Quantitative Medicine
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| Street address |
1500 E. Duarte Rd.
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| City |
Duarte |
| State/province |
CA |
| ZIP/Postal code |
91010 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE95654 |
DNA methylation analysisof KRAS mutated colorectal tumors and adjacent tissues from cancer patinets and KRAS mutated Aberrant Crypt Foci and matching normal crypts from healthy individuals by using RRBS |
| GSE95656 |
Genome-wide DNA methylation profiling reveals cancer-associated changes within early colonic neoplasia |
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| Relations |
| BioSample |
SAMN06473295 |
| SRA |
SRX2611092 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2520760_6377_178_N_GAGTGG_L004_R1_001_val_1.fq_bismark_pe.bedGraph.gz |
46.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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