|
| Status |
Public on Mar 01, 2019 |
| Title |
ATAC_SCC1_shPitx1_1 |
| Sample type |
SRA |
| |
|
| Source name |
ATAC_SCC1_shPitx1
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
tissue: skin
tissue subtype: squamous cell carcinoma (SCC)
|
| Growth protocol |
15,000 cells were injected intradermally to form tumor allografts. In the end point of the experiment, 50,000 cells were sorted gatting in integrin α6 and integrin b1
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 tumor-propagating cells (TPCs) were isolated by FACS and washed once with cold 1x PBS. Cells were pelleted and lysed in 50 μl and spun at 500g for 25min at 4C to collect nuclei. Pelleted nuclei were incubated for 30min at 37 C with 2.5ul of Tn5 transposase (Illumina Cat #FC-121-1030) before transposed DNA fragments were purified with a Qiagen MinElute Kit for ATAC-seq library generation.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ATAC_SCC_1_shPixt1_Hi_1_S11_L001
|
| Data processing |
Mouse assembly version mm10/NCBI m38 build were used for sequence alignments with bowtie 45 version 2.1.0.
ATAC-seq peaks were called with PeaKDEck55 and the parameter (-sig 0.0001).
Genome_build: mm10
Supplementary_files_format_and_content: File with PeakDEck peak calling
|
| |
|
| Submission date |
Jan 23, 2019 |
| Last update date |
Mar 01, 2019 |
| Contact name |
Markus Schober |
| E-mail(s) |
markus.schober@nyulangone.org
|
| Organization name |
New York University School of Medicine
|
| Department |
Dermatology
|
| Street address |
550 First Ave, Smilow 407
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE104136 |
Defining transcription factor networks that govers SCC growth [ATAC-seq] |
| GSE104145 |
Defining transcription factor networks that govers SCC growth |
|
| Relations |
| BioSample |
SAMN10792977 |
| SRA |
SRX5283001 |
