|
| Status |
Public on Apr 19, 2023 |
| Title |
S2-VP10_CUT&RUN_H3K4me1 |
| Sample type |
SRA |
| |
|
| Source name |
Pancreatic adenocarcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: S2-VP10 (human pancreatic adenocarcinoma)
model: 2D culture cell
cut&run antibody: anti-H3K4me1 (Abcam, ab8895)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed using the CUT&RUN Assay Kit (CST) with a modification of the manufacturer’s protocol.
Libraries were prepared using NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs).
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
S2VP10_H3K4me1_H3K27ac_overlapped.bed
|
| Data processing |
Library strategy: CUT&RUN
Basecalls and conversion to FASTQ files were performed using Basesapce online (Illumina).
Sequencing reads were trimmed for adaptor sequence, and aligned to human genome (hg19) by Bowtie2 (version 2.3.4.1).
Duplicate reads were removed.
The number of unique reads was normalized to spike-in yeast DNA (sacCer3).
CUT&RUN data were converted to bigwig files by bamCoverage (in the deepTools package, version 3.5.1) with the following parameters: --scaleFactor <each sample> --binSize 10.
Peak detection was performed using MACS2 59 (version 2.2.7.1) with default parameters.
The Overlapping peaks between H3K4me1 and H3K27ac were obtained using the bedtools intersect function (version 2.30.0).
Genome_build: hg19
Supplementary_files_format_and_content: Bigwig files. BED files.
|
| |
|
| Submission date |
Dec 18, 2021 |
| Last update date |
Apr 19, 2023 |
| Contact name |
Masaya Yamazaki |
| E-mail(s) |
myamazaki@kumamoto-u.ac.jp
|
| Organization name |
Kumamoto university
|
| Lab |
Medical Biochemistry
|
| Street address |
1-1-1, Honjyo, Chuo-ku
|
| City |
Kumamoto city |
| ZIP/Postal code |
860-8556 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE191202 |
Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma [CUT&RUN] |
| GSE191204 |
Single-cell RNA-sequencing reveals an intratumor heterogeneity in pancreatic adenocarcinoma |
|
| Relations |
| BioSample |
SAMN24196314 |
| SRA |
SRX13446124 |
