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| Status |
Public on Oct 05, 2021 |
| Title |
empty_rep2 |
| Sample type |
SRA |
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| Source name |
ASZ
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| Organism |
Mus musculus |
| Characteristics |
cell line: ASZ
treatment: N/A
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| Treatment protocol |
ASZ cells with dox-inducible c-FOS construct were treated with doxycycline in serum-free medium for 24h. Cells were then treated with either 5µM of afatinib, 10µM of UO126 or DMSO for 6h. ASZ cells with an empty construct were treated with doxycycline in serum-free medium for 24h as the control. Following the inhibition assay, cells were harvested for ATAC-seq.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq cell lysis and transposition with Tn5 was carried out based on published protocol by Buenrostro et. al (Nature Methods, 2013) with minor modifications for on-plate transposition. Briefly, 50,000 ASZ001 cells were plated per replicate in a 48-well plate, then serum starved for 24 hours. Wells were washed with cold PBS and lysed using 0.1% NP40 in resuspension buffer for 10 minutes at 25°C. Wells were washed again, then 100 µl of transposition mixture was added per well and incubated for 37°C for 30 min, shaking at 1000 RPM using a thermoshaker. DNA was purified using the Qiagen MinElute columns per manufacturer's instructions.
Libraries were generated using custom Nextera PCR primers and PCR conditions from published protocol by Buenrostro et. al (Nature Methods, 2013).
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
bowtie2 used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
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| Submission date |
Jun 25, 2021 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Anthony Oro |
| Organization name |
Stanford University
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| Department |
Dermatology
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| Street address |
269 Campus Drvie
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE168376 |
C-FOS-driven basal to squamous cell transition |
| GSE178914 |
Chromatin accessibility changes in experimentally-induced basal to squamous cell carcinoma transition (BST) upon EGFR/MAPK inhibitor treatments [ASZ_ATACseq_inhibitor] |
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| Relations |
| SRA |
SRX11230174 |
| BioSample |
SAMN19896455 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5400807_empty_2_norm.bw |
193.6 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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