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| Status |
Public on Mar 31, 2022 |
| Title |
Normal sample of Monkey RM40 (RRBS) |
| Sample type |
SRA |
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| Source name |
COLON
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| Organism |
Macaca mulatta |
| Characteristics |
tissue: Normal
msi status: MSI-H
sample id: RM40
gender: Female
mlh1 c.1029 (c>g) germline mutation status: Wild type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Macro-dissection was performed to decrease the admixture of adjacent normal tissue and to enrich the percentage of tumor material for subsequent RNA extraction. De-paraffinization of FFPE tumor and adjacent normal specimens was performed using QIAGEN de-paraffinization solution (QIAGEN, Valencia, CA). DNA and RNA from 19 tumor and adjacent normal samples was extracted using the AllPrep DNA/RNA FFPE Kit (QIAGEN) following the manufacturer’s protocol. In the case of the unavailability of FFPE samples, genomic DNA and RNA were extracted from fresh frozen tumor (n=2) and normal (n=3) samples using the ZR-Duet DNA/RNA MiniPrep extraction kit (ZYMO RESEARCH, Irvine, CA). Quantification was performed with a NanoDrop One™ spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and Qubit™ Fluorometer 2.0 (Qubit, San Francisco, CA) using dsDNA and RNA assay kits. RNA integrity was analyzed using the Tape Station RNA assay kit (Agilent Technologies, Santa Clara, CA).
DNA libraries of RRBS were constructed from FFPE tissue samples of 14 tumors/adjacent normal tissue pairs using the Ovation RRBS Methyl-Seq System at The Epigenomics Profiling Core (EpiCore) of MDACC. In preparation, DNA was digested with a restriction enzyme and selected for size based on established protocols used in the EpiCore. Post-adapter ligation ensured enrichment for CpG islands, and DNA was bisulfite-treated, amplified with universal primers, and qualified libraries were then sequenced on Novaseq6000™ and MiSeq sequencers at the UTMDACC ATG
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
FASTQC toolkit was performed for quality control of FASTQ files
TrimGalore was performed to trim adapters and low-quality reads
Diversity trimming and filtering were completed with NuGEN’s diversity trimming scripts
Processed fastq files were aligned to the reference genome (Mmul_10) with bismark bisulfite mapper.
The methylation information was extracted with bismark methylation extractor script.
Genome_build: Mmul_10
Supplementary_files_format_and_content: bedGraph file with the estimated methylation rate
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| Submission date |
Jun 17, 2021 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Eduardo Vilar-Sanchez |
| Organization name |
The University of Texas MD Anderson Cancer Center
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| Street address |
1515 Holcombe Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL27943 |
| Series (2) |
| GSE178377 |
Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer (RRBS) |
| GSE178383 |
Rhesus Macaque Model of Mismatch Repair-Deficient Colorectal Cancer |
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| Relations |
| BioSample |
SAMN19761608 |
| SRA |
SRX11171987 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5389302_NOL16.bedGraph.gz |
253.9 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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