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| Status |
Public on Jan 17, 2024 |
| Title |
Hela-OLDN-fragments-rep2 |
| Sample type |
SRA |
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| Source name |
Hela cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: Hela
sample group: OLDN-fragments
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| Growth protocol |
The HeLa cells were commercially obtained and stored at -80ºC until use.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The HeLa cells were suspended in the washing solution containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, and a proteinase inhibitor (Roche). The detergent buffer containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, proteinase inhibitor (Roche), and 1% NP-40 was then added to the cell suspension, and the mixture was rotated at 4 ºC for 10 minutes. The HeLa nuclei were collected by centrifugation and were resuspended in the washing solution. A large amount of MNase (3 units/µL) and CaCl2 (2 mM) were added to the HeLa nuclei suspension. The MNase treatment was performed under 37 ºC for 30 minutes, and was terminated by EDTA (pH 8.0) addition. The MNase fragments were precipitated by ethanol, and were electrophoresed by 4% agarose gel.
Libraries were prepared using ThruPLEX DNA-Seq Kit (Clontech, #R400674).
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
200-300 bp DNA fragmants were sampled
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| Data processing |
Adapter DNAs were trimmed using Trim Galore (version 0.6.7) with the options: --paired.
The paired-end reads were mapped to the GRCh38 for the Hela samples and the tandemly connected three Widom 601 sequences for the in vtiro sample using bowtie (version 2.3.5.1) with the default options.
Data of Hela samples were filtered using the following specifications; OLTN: 337 (+/- 5) bp, OLDN: 248 (+/- 5) bp and mono-nucleosome: 147 (+/- 5) bp, respectively.
For Hela data, the bigWig files were created by 50 bp intervals on the genome, and then the counts were normalized as CPM (Reads Per Million reads) using deepTools (version 3.5.1) with the option: -bs 1 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates --normalizeUsing CPM.
For in vitro data, a count file was created by counting fragments by lengths.
Assembly: GRCh38
Supplementary files format and content: bigwig files were genelated using deepTools (version 3.5.1, bamCoverage function) with the option
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| Submission date |
Feb 08, 2023 |
| Last update date |
Jan 17, 2024 |
| Contact name |
Yasuyuki Ohkawa |
| E-mail(s) |
yohkawa@bioreg.kyushu-u.ac.jp
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| Organization name |
Medical Institute of Bioregulation
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| Lab |
Division of Transcriptomics
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| Street address |
3-1-1 Maidashi
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| City |
Fukuoka |
| ZIP/Postal code |
8128582 |
| Country |
Japan |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE224789 |
Analysis of the overlapping tri-nucleosome association with genomic and synthetic DNA |
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| Relations |
| BioSample |
SAMN33208976 |
| SRA |
SRX19312004 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7032267_Hela-MNase-OLDN-2-243-253.bw |
70.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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