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| Status |
Public on Dec 13, 2016 |
| Title |
Culture_SHPCBclone_rep2 |
| Sample type |
SRA |
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| Source name |
Culture_SHPCBclone
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| Organism |
Homo sapiens |
| Characteristics |
gender: Female
cell line: SH-SY5Y
cell type: human neuroblastoma cell line
treated with: PCB 95 in DMSO for 10 days
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| Treatment protocol |
1 μM PCB 95 in 0.1% DMSO for 40 days. Then, clonally isolated and grown for 21
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.). 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 |
JLKD044
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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
|
| 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 |
SAMN05006641 |
| SRA |
SRX1770523 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2157022_JLKD044.bed.gz |
156.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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