|
| Status |
Public on Mar 07, 2022 |
| Title |
MKL-1 Vehicle IgG - Rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
MKL-1 Merkel cell carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 1% ethanol
cut&run antibody: 1:100 rabbit anti-mouse IgG (Abcam ab46540)
cell line: MKL-1
|
| Treatment protocol |
36E4 cells were plated at 12E4 cells/mL with 1% ethanol or 3 µM EPZ011989 in a final concentration of 1% ethanol. Cells were split approximately 1:2 into larger dishes with complete media refreshment on day 3 and harvested on day 6.
|
| Growth protocol |
MKL-1 cells were maintained in RPMI medium with 10% FBS at 37 °C and 5% CO2.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were treated with Accutase and samples were split into thirds, bound to ConA beads, and permeabilized with 0.025% digitonin. Antibodies were added for overnight incubation at 4 °C. After 30 min incubation with pA-Mnase plus calcium, stop buffer containing RNase A and 200 pg/mL E. coli spike-in DNA was added. DNA was extracted using a standard phenol/chloroform protocol.
Libraries were constructed using automated Swift 2S ligation chemistry.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: CUT&RUN
Illumina basecalling was performed by the Dana-Farber Cancer Institute Molecular Biology Core Facilities.
Read quality was checked by FastQC.
Files were aligned separately to hg38 and E. coli K-12 GCA_004919995 using bowtie 2 version 2.2.9 with commands --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Samtools version 0.1.19 view was used to downsample the aligned human reads according to the number of aligned E. coli reads per sample. Bam files were converted to .bw
Macs2 version 2.1.1.20160309 was used to call peaks with the following options: For H3K4me3 and IgG narrowPeak files were generated: -q 0.05 -f BAMPE --keep-dup all --nolambda; For H3K27me3 broadPeak files were generated: -q 0.05 -f BAMPE --keep-dup all --nolambda --broad --broad-cutoff 0.1
Genome_build: hg38 and E. coli K-12 GCA_004919995
Supplementary_files_format_and_content: .bw files contain downsampled aligned read pileups for each sample; .narrowPeak and .broadPeak files contain genome coordinates, scores, and p-values called by macs2 for each sample.
|
| |
|
| Submission date |
Nov 01, 2021 |
| Last update date |
Mar 07, 2022 |
| Contact name |
Ashley K. Gartin |
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
DeCaprio Lab
|
| Street address |
450 Brookline Ave. Mayer 444
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE186897 |
Next-generation sequencing of CUT&RUN of MKL-1 Merkel cell carcinoma cells treated with EPZ011989 |
| GSE186899 |
MKL-1 Merkel cell carcinoma cells treated with EPZ011989 |
|
| Relations |
| BioSample |
SAMN22815175 |
| SRA |
SRX12875507 |
