|
| Status |
Public on Sep 01, 2021 |
| Title |
ATAC-seq_Melanoma_p44_STAT3_KO_113-2_1 |
| Sample type |
SRA |
| |
|
| Source name |
Melanoma cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Melanoma cell line
genotype/variation: STAT3 knockout
clone: 113
biological replicate: 2
|
| Growth protocol |
Mouse melanoma cell lines were established from primary lymph node single cell suspensions from diseased mice with cutaneous melanoma onset around 25-30 weeks of age. Multiple individual primary pools of cell lines per Stat3fl and Stat3∆ melanoma cell genotype were generated, upon which we selected two pools each for further detailed analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Duplicates of two different STAT3fl and STAT3∆ cell lines were used for the assay. A volume containing 50.000 cells were harvested with the aid of an automated cell counter (TC20 Bio-Rad) and spun at 500g for 5 minutes at 4°C in PBS.
After centrifugation, the pellet was carefully resuspended in the transposase reaction mix (12.5 µl 2xTD buffer, 2 µl TDE1 (Illumina), and 10.25 µl nuclease-free water, 0.25 µl 1% Digitonin (Sigma)) for 30 min at 37 °C. Following DNA purification with the MinElute kit eluting in 12 µl, 1 µl of the eluted DNA was used in a quantitative PCR reaction to estimate the optimum number of amplification cycles. Library amplification was followed by SPRI size selection to exclude fragments larger than 1,200 bp. DNA and concentration was measured with a Qubit fluorometer (Life Technologies). Library amplification was performed using custom Nextera primers.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
ATAC-seq of mouse melanoma cell with STAT3 knockout, clone 113, biological replicate 2.
processed data file: melanoma_stat3_peaks.raw_coverage.csv
|
| Data processing |
Illumina Casava1.7 software was used for basecalling.
Sequenced reads were trimmed for adaptor and Nextera sequences.
Reads were mapped to mm10 genome using bowtie2 v2.2.4 with the –very-sensitive parameter.
Duplicate reads were marked and removed with picard tools version 1.118.
Read were extended to the average fragment size and bigWig files containing counts of reads per basepair created.
Peaks for ATAC-seq samples were called with MACS2 version 2.1.1.20160309 using the “–nomodel” and “–extsize 147” parameters.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bigWig files contain counts of reads per basepair.
Supplementary_files_format_and_content: narrowPeak files contain peaks called by MACS2.
Supplementary_files_format_and_content: melanoma_stat3_peaks.raw_coverage.csv: Comma-separated text file with raw read counts per sample per regulatory element.
|
| |
|
| Submission date |
Sep 05, 2018 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Christoph Bock |
| E-mail(s) |
cbock@cemm.oeaw.ac.at
|
| Organization name |
CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
|
| Street address |
Lazarettgasse 14
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE119540 |
STAT3 promotes melanoma metastasis by CEBP-induced repression of the MITF pigmentation pathway |
|
| Relations |
| BioSample |
SAMN09981024 |
| SRA |
SRX4644742 |
