|
| Status |
Public on Oct 05, 2021 |
| Title |
ASZ_RasV12_TGFbR1-kd_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
ASZ_ RasV12_TGFbR1-kd/Dox-4OHT
|
| Organism |
Mus musculus |
| Characteristics |
treatment: 6 days Dox/4OHT
genotype: RasV12_TGFbR1-kd
cell line: ASZ001
|
| Growth protocol |
ASZ001 cells were cultured in 154CF medium (Life Technologies) supplemented with 2% chelated FBS and 0.05 mM CaCl2.
|
| 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).
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
bowtie used for alignment.
duplicate fragments were removed using samtools
macs2 used for peak calling
Genome_build: mm9
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Nov 06, 2020 |
| Last update date |
Oct 05, 2021 |
| Contact name |
Anthony Oro |
| Organization name |
Stanford University
|
| Department |
Dermatology
|
| Street address |
269 Campus Drvie
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE161009 |
Chromatin accessibility changes in experimentally-induced basal to squamous cell carcinoma transition (BST) |
| GSE168376 |
C-FOS-driven basal to squamous cell transition |
|
| Relations |
| BioSample |
SAMN16688207 |
| SRA |
SRX9451521 |
