|
| Status |
Public on Sep 04, 2020 |
| Title |
7.1_DMSO_d6_H3K27ac |
| Sample type |
SRA |
| |
|
| Source name |
PeTa_DMSO_H3K27ac
|
| Organism |
Homo sapiens |
| Characteristics |
cell line name: PeTa
cell type: Merkel cell carcinoma cell line
drug: DMSO
antibody: anti-H3K27ac (ab4729, Abcam, 1:50)
|
| Treatment protocol |
Cells were treated with 100 nM GSK-LSD1 for 6 days or DMSO.
|
| Growth protocol |
Cells were cultured as suspension cells in RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 50 U/mL penicillin and 50 mg/mL streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CUT&RUN was performed according to the high-calcium/low-salt digestion protocol described previously (Meers et al. 2019).
The antibodies used in our CUT&RUN studies are anti-rabbit IgG isotype (ABIN101961, Antibodies online, 1:50), anti-H3K4me1 (C15410194, Diagenode, 1:50), anti-H3K27ac (ab4729, Abcam, 1:50) and anti-H3K27me3 (9733, CST, 1:50).
CUT&RUN libraries were prepared with the NEBNext® Ultra II DNA Library Prep Kit.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
7.1_DMSO_d6_H3K27ac.bam.R1_val
processed data file: DMSO_d6_H3K27ac.bam.normalized.bw
|
| Data processing |
library strategy: CUT&RUN
CUT&RUN data was analyzed utilizing the nf-core(Ewels et al. 2020) ChIPSeq pipeline(Wang et al. 2019) using the human genome hg38 and calling peaks in broad-peak mode.
Aligned reads of the individual replicates were merged using samtools v1.9(Li et al. 2009) and RPGC-normalized tracks were calculated and plotted as composite density plots using deeptools v3.1.2(Ramírez et al. 2016).
Genome_build: hg38
Supplementary_files_format_and_content: RPGC-normalized bigWig tracks
|
| |
|
| Submission date |
Apr 05, 2020 |
| Last update date |
Sep 04, 2020 |
| Contact name |
Anna Obenauf |
| Organization name |
IMP - Research Institute of Molecular Pathology
|
| Lab |
Anna Obenauf
|
| Street address |
Campus-Vienna-Biocenter 1
|
| City |
Vienna |
| State/province |
Vienna |
| ZIP/Postal code |
1030 |
| Country |
Austria |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE147817 |
Pharmacological LSD1 inhibition in MCC |
| GSE148103 |
Chromatin profiling upon pharmacological LSD1 inhibition in MCC [CUT&RUN] |
|
| Relations |
| BioSample |
SAMN14542027 |
| SRA |
SRX8060930 |
