|
| Status |
Public on Apr 06, 2020 |
| Title |
Cont papilloma (5) |
| Sample type |
SRA |
| |
|
| Source name |
Papilloma-derived cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Whole papillomas
induction period: 27wks-age mice
profiled cells: Papilloma-derived cells
genotype/variation: Control
|
| Treatment protocol |
Whole papillomas were dissected.
|
| Growth protocol |
3-week-old K5-rtTA/tet-p16 and control tet-p16 mice received a single topical treatment of 50nmole DMBA. A week later dox was added to the drinking water and the mice began twice-weekly topical treatments with TPA. Mice were examined for 23 additional weeks and were sacrificed 10 days after the last TPA treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from whole papillomas using the Tissue RNA purification kit (Norgen Biotek)
Libraries were prepared using the CEL-Seq protocol, and sequenced on Illumina HiSeq 2500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
p16_expressing_versus_control_skin_papillomas.xlsx
|
| Data processing |
Reads containing adapters and poly-A sequences were trimmed using Cutadapat.
Genome mapping was performed using Tophat2, and read counts summarized through HTSeq count
Normalization was performed on the counts using DESeq2
Genes found not to be expressed in sorted keratinocytes (series 1,2) were excluded from analysis.
Genome_build: GRCm38
Supplementary_files_format_and_content: An Excel file with headers. The column ‘Expressed in sorted keratinocytes’ indicates whether the gene was found in sorted keratinocytes (series 1,2) and hence included in our final analysis. ‘Norm.’ columns are the values after DESeq2 normalization. Log2FoldChange, lfcSE, stat, pvalue, padj are the results of DESeq2 analysis.
|
| |
|
| Submission date |
Mar 13, 2020 |
| Last update date |
Apr 06, 2020 |
| Contact name |
Ittai Ben-Porath |
| E-mail(s) |
ittaibp@mail.huji.ac.il
|
| Organization name |
The Hebrew University Faculty of Medicine
|
| Department |
Department of Developmental Biology and Cancer Research
|
| Street address |
Ein-Kerem
|
| City |
Jerusalem |
| State/province |
N/A |
| ZIP/Postal code |
91120 |
| Country |
Israel |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE146978 |
Chronic expression of p16INK4a in the epidermis induces Wnt-mediated hyperplasia and promotes tumor initiation (2) |
| GSE146979 |
Chronic expression of p16INK4a in the epidermis induces Wnt-mediated hyperplasia and promotes tumor initiation |
|
| Relations |
| BioSample |
SAMN14376621 |
| SRA |
SRX7911212 |
