|
| Status |
Public on May 24, 2022 |
| Title |
MA9_ATACseq |
| Sample type |
SRA |
| |
|
| Source name |
Sorted melanoma tumor
|
| Organism |
Danio rerio |
| Characteristics |
genotype: BRAFV600E/p53lf/lf/crestin:EGFP
tissue: Melanoma
run #: 3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
FACS for fluorescent tag: mCherry for melanocytes (MC) and GFP for melanoma cells (MA)
Up to 50,000 cells were tagmented with an Illumina Nextera kit and purified with a Qiagen MinElute Purification Kit. DNA was amplified with a 9x cycling protocol combined with bead purification of proper sized fragments.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Melanoma cells
|
| Data processing |
Demultiplex and trim reads with Cutadapt
Align reads to GRCz10/danRer11 using BWA-MEM
Remove duplicate reads with GATK
Index and filter for high quality reads with SAMtools and bamtools
Identify peaks with MACS2 callpeak function
Genome_build: danRer11
Supplementary_files_format_and_content: bigwig and narrowPeak files generated
|
| |
|
| Submission date |
Jun 24, 2021 |
| Last update date |
May 24, 2022 |
| Contact name |
Charles K Kaufman |
| E-mail(s) |
ckkaufman@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Oncology
|
| Lab |
Kaufman
|
| Street address |
660 S Euclid Ave
|
| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL18413 |
| Series (2) |
| GSE178802 |
Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors [ATAC-seq] |
| GSE178803 |
Transcriptional Profile and Chromatin Accessibility in Zebrafish Melanocytes and Melanoma Tumors |
|
| Relations |
| BioSample |
SAMN19845289 |
| SRA |
SRX11217402 |
