 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 06, 2023 |
| Title |
HBEC3 cells, Empty vector |
| Sample type |
SRA |
| |
|
| Source name |
HBEC3-KT
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HBEC3-KT
cell type: Human Bronchial cells
genotype: Empty Vector
|
| Growth protocol |
keratinocyte SFM medium , Cells were cultured at 37C at 5% CO2.
|
| 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
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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
|
| |
|
| Submission date |
Jul 20, 2022 |
| Last update date |
Jul 06, 2023 |
| Contact name |
Gerd Pfeifer |
| E-mail(s) |
gerd.pfeifer@vai.org
|
| Organization name |
Van Andel Research Institute
|
| Street address |
333 Bostwick Ave. NE
|
| City |
Grand Rapids |
| State/province |
MI |
| ZIP/Postal code |
49503 |
| Country |
USA |
| |
|
| 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 |
|
| Relations |
| BioSample |
SAMN29855157 |
| SRA |
SRX16367684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6364295_WGBS_Ctrl2.bw |
178.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
