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| Status |
Public on Jun 22, 2018 |
| Title |
WCM154 PDOX |
| Sample type |
SRA |
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| Source name |
WCM154 PDOX
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| Organism |
Homo sapiens |
| Characteristics |
tissue: prostate organoid
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| Treatment protocol |
No treatments were applied prior to genomic DNA extraction
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| Growth protocol |
In brief, the preparation steps included: 1) MspI enzyme digestion; 2) end repair of digested DNA;3) adenylation; 4) adapter ligation, with pre-annealed 5-methylcytosine–containing Illumina adapters; 5) isolation of library fragments of 150 to 400 bp from a 1.5% agarose gel (using low-range ultra-agarose from Bio-Rad, Des Plaines, IL); 6) bisulfite conversion using the EZ DNA Methylation Kit (Zymo Research, Irvine, CA) with the following changes: i) CT conversion incubation in a thermocycler (Eppendorf, Hauppauge, NY) with the condition: 30 seconds at 95°C followed by 15 minutes at 50°C for 55 cycles, and ii) elution into nuclease-free water; 7) polymerase chain reaction (PCR) amplification; each library was prepared with FastStart High Fidelity DNA Polymerase (Roche, Indianapolis, IN) and Illumina PCRprimers PE1.0 and 2.0.The thermocycler conditions were given as follows: 5 minutes at 94°C, 18 cycles of 20 seconds at 94°C, 30 seconds at 65°C, 1 minute at 72°C, followed by 3 minutes at 72°C. PCR products were isolated using Agencourt AMPure XP (Beckman Coulter, Brea, CA) beads per manufacturer’s recommended protocol (Agencourt) All amplified libraries were evaluated using a Qubit 1.0 fluorometer and Quant-iT dsDNA HS Assay Kit (Invitrogen, Grand Island, NY) for quantitation and bioanalyzer visualization (Agilent 2100 Bioanalyzer; Agilent, Santa Clara, CA).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extractions from organoids and PDOXs were performed using DNeasy Blood and Tissue Kit (QIAGEN) and Maxwell 16 Tissue DNA Purification Kit (Promega). .
errbs
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| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
FASTQ files were generated by using the Illumina CASAVA 1.8.2 pipeline.
Briefly, bisulfite reads were aligned to the bisulfite-converted hg19 reference genome using Bismark.
Genome_build: hg19
Supplementary_files_format_and_content: methylcall files are in .txt format
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| Submission date |
Apr 06, 2018 |
| Last update date |
Jun 22, 2018 |
| Contact name |
Himisha Beltran |
| E-mail(s) |
hip9004@med.cornell.edu
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| Organization name |
Weill Cornell Medicine
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| Street address |
413 East 69th Street
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| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10021 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (2) |
| GSE112829 |
Methylation profile of neuroendocrine prostate cancer models |
| GSE112830 |
Neuroendocrine prostate cancer models |
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| Relations |
| BioSample |
SAMN08886704 |
| SRA |
SRX3899242 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3084577_cpg.PDOXWCM154.mincov10.txt.gz |
28.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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