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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 05, 2024 |
| Title |
hFB cells, WGBS, DMSO, BR2 |
| Sample type |
SRA |
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| Source name |
skin
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| Organism |
Homo sapiens |
| Characteristics |
tissue: skin
cell line: HDFa
cell type: primary dermal fibroblast
treatment: DMSO
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
We extracted genomic DNA with Quick-DNA Miniprep Kit (Zymo, D3024)
We bisulfite converted 200-400 ng of DNA spiked with 0.5% lambda DNA using EZ DNA Methylation-Direct kit (Zymo, D5020). For WGBS, we processed the bisulfite- converted DNA with Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024).
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| Library strategy |
Bisulfite-Seq |
| Library source |
transcriptomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw sequencing reads are trimmed using TrimGalore (v.0.6.1) with "-a AGATCGGAAGAGC".
Bismark (v.0.22.0) was used to prepare bisulfite-converted hg38 reference genome and to align trimmed reads to the prepared genome (-X 2000 --nucleotide_coverage).
Uniquely mapped, deduplicated reads were retained.
hg38
bed (methylC)
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| Submission date |
Mar 09, 2023 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
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| Phone |
(314) 286-0866
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| Organization name |
Washington University in St. Louis
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| Department |
Genetics
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| Lab |
Ting Wang Lab
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| Street address |
4515 McKinley Avenue
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| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE227059 |
Epigenetic therapy activates TE-chimeric transcripts to provide additional source of antigens in glioblastoma stem cells |
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| Relations |
| BioSample |
SAMN33706477 |
| SRA |
SRX19626996 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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