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| Status |
Public on Jul 06, 2023 |
| Title |
HBEC3 cells, WT, RYBP |
| 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: Wild type
chip antibody: RYBP(millipore, AB3637)
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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 |
For RYBP ChIP, cells were fixed with 2.5 mM EGS (ethylene glycol-bis-succinimidyl-succinate) for 45 minutes, then fixed with 1% formaldehyde for 8 minutes; for H2AK119ub1 and H3K27me3, cells were crosslinked with 1% formaldehyde only for 8 minutes, after quenching and cell lysis, chromatin was sonicated using a Covaris E220 Evo sonicator.
TruSeq ChIP Sample Preparation Kit (Illumina, IP-202-1012, IP-202-1024) was used according to the manufacturer’s instructions to perform ChIP-seq library preparation. 5 ng of DNA was used as starting material for input and IP samples. Libraries were amplified using 14 cycles on the thermocycler. Libraries were validated using the Agilent High Sensitivity DNA Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
75-bp single-end reads were trimmed with Trim Galore (version 0.4.0) with default parameters, then the trimmed reads were mapped to human genome hg19 with Bowtie2(version 2.3.5)
The aligned reads were deduplicated with the software picard(version 2.19.0)
Then the deduplicated reads were used for peak calling by HOMER (version 4.10) with the following settings: -B -region -size 1000 -minDist 2500 -P 0.01 -F 2.0 -L 2.0 -LP 0.01.
Output bedgraph files from HOMER were processed into bigwig files with UCSC Exe Utilities bedGraphToBigWig(version 1.04.00)
Assembly: hg19
Supplementary files format and content: bigWig, counts coverage
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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 |
GPL18573 |
| Series (2) |
| GSE208687 |
Dysfunction of 5-methylcytosine oxidases and the Polycomb protein RYBP leads to widespread DNA hypermethylation and cell transformation [ChIP-seq] |
| 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 |
SAMN29855248 |
| SRA |
SRX16367657 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6364268_RYBP_Ctrl1.bw |
275.1 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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