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Status |
Public on Dec 13, 2016 |
Title |
Culture_SH15Mdup22_rep3 |
Sample type |
SRA |
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Source name |
Culture_SH15Mdup22
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Organism |
Homo sapiens |
Characteristics |
gender: Female cell line: SH-SY5Y-15Mdup22 cell type: human neuroblastoma cell line with extra copy of part of maternal chr15 and part of chr22 treated with: DMSO for 40 days
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Treatment protocol |
0.1% DMSO for 40 days. Then, clonally isolated and grown for 21 generations. None unless specified
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Growth protocol |
Grown in Dulbecco’s modified Eagle’s medium, DMEM/F12 medium supplemented with 15% fetal bovine serum (GIBCO, Gaithersburg, MD, U.S.A.) with the addition of 800 μg/ml G 418 to stably maintain 15M duplicated chromosome. Cells were maintained at 37°C in a saturated humidity atmosphere containing 95% O2 and 5% CO2. Cells were seeded at an initial density of 1.5 x 106 cells in T75 Flask. None unless specified
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Extracted molecule |
genomic DNA |
Extraction protocol |
Extracted and purified using the Qiagen Puregene kit Five (5) μg of DNA was fragmented to ~300 bp using 28 cycles of 15 seconds on/15 seconds off on a Diagenode Bioruptor. DNA was end-repaired using 1× T4 DNA ligase buffer, 400 μM dNTPs, 15 U T4 DNA polymerase (NEB), and 50 U PNK (NEB) for 30 min at 20°C. After PCR purifying (Qiagen), adenine bases were appended to the ends using 1× NEB 2 buffer, 200 μM dATP, and 15 U Klenow Fragment (3′ to 5′ exo-, NEB) for 30 min at 37°C. After another DNA purification using the PCR MinElute kit (Qiagen), 3 μL of Illumina's methylated sequencing adapters were ligated on using 1× ligase buffer and 5 μL Quick T4 DNA Ligase (NEB) for 30 min at room temperature. After a final PCR purification, 500 ng of library was bisulfite converted using Zymo's EZ DNA Methylation-Direct kit according to the manufacturer's instructions. The library was then amplified using 2.5 U PfuTurbo Cx Hotstart DNA Polymerase (Stratagene) for 12 cycles using Illumina's standard amplification protocol.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
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Description |
JLKD049
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Data processing |
Filter using Illumina flag Separate and trim reads based on adapter contamination Align to hg38 using BSSeeker2 Combine aligned reads, both trimmed and no adapter contamination Convert sam files to percent methylation bed files Combine all chromosome percent methylation bed files into a single file Genome_build: hg38 Supplementary_files_format_and_content: Percent Methylation Bed file containing single base methylation information with ranged color coding
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Submission date |
May 17, 2016 |
Last update date |
May 15, 2019 |
Contact name |
Keith Dunaway |
E-mail(s) |
kwdunaway@ucdavis.edu
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Organization name |
UC Davis
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Department |
MMI
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Lab |
LaSalle Lab
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Street address |
3318 Tupper Hall
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City |
Davis |
State/province |
CA |
ZIP/Postal code |
95616 |
Country |
USA |
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Platform ID |
GPL11154 |
Series (1) |
GSE81541 |
Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes. |
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Relations |
BioSample |
SAMN05006643 |
SRA |
SRX1770527 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2157026_JLKD049.bed.gz |
170.7 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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