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| Status |
Public on Jul 06, 2023 |
| Title |
HBEC3 cells, RYBP/T123 QKO1 |
| Sample type |
SRA |
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| Source name |
HBEC3-KT
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HBEC3-KT
cell type: Human Bronchial cells
genotype: RYBP,TET1,TET2,TET3 quadruple knockout
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| Growth protocol |
keratinocyte SFM medium , Cells were cultured at 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted using a Quick-DNA Miniprep Plus kit (Zymo Research, D4070).
The Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, 30024) was used according to the manufacturer’s instructions to perform bisulfite conversion and library preparation.
WGBS
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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 |
Paired-end reads were trimmed using TrimGalore(version 0.5.0) with the following parameters : --length 50, --clip_R1 10, --clip_R2 18, --three_prime_clip_R1 10, and --three_prime_clip_R2 10.Â
Trimmed reads were aligned to the hg19 using Bismark version 0.19.0
Duplication were removed using the deduplicate_bismark script provided with Bismark
CpG methylation values were called by the bismark_methylation_extractor script provided with Bismark and the following parameters: --no_overlap, --comprehensive, --merge_non_CpG, and --cytosine_report.
Assembly: hg19
Supplementary files format and content: bigWig, methylation coverage with cutoff 3
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| Submission date |
Jul 20, 2022 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Gerd Pfeifer |
| E-mail(s) |
gerd.pfeifer@vai.org
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| Organization name |
Van Andel Research Institute
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| Street address |
333 Bostwick Ave. NE
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| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE208688 |
Dysfunction of 5-methylcytosine oxidases and the Polycomb protein RYBP leads to widespread DNA hypermethylation and cell transformation [WGBS] |
| GSE208689 |
Dysfunction of 5-methylcytosine oxidases and the Polycomb protein RYBP leads to widespread DNA hypermethylation and cell transformation |
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| Relations |
| BioSample |
SAMN29855174 |
| SRA |
SRX16367701 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6364312_WGBS_RT123_QKO1.bw |
183.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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