|
| Status |
Public on Aug 30, 2019 |
| Title |
MCFDCIS tumor treated with vehicle, initial response (2V-096L) |
| Sample type |
SRA |
| |
|
| Source name |
MCFDCIS Hsapiens cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCFDCIS
treatment: Vehicle
Stage: initial
|
| Treatment protocol |
Animals were treated daily with 50mg/kg Palbociclib by oral gavage
|
| Growth protocol |
1 Million MCFDCIS cells were injected subcutaneously into Athymic Nude Mice and given 2 weeks to establish DCIS tumors in the animals prior to treatment initiation
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy extraction following tumor homogenization using the Roche MagNA Lyser
TruSeq RNA Library Prep
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
2wk Vehicle
|
| Data processing |
Casava v1.8 basecalling
cutadapt adapter removal, demux
STAR RNAseq alignment to GRCh38, GRCm38, params: --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 –outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 –quantMode GeneCounts --twopassMode Basic --twopassMode Basic
Normalization, differential expression in R with edgeR
Genome_build: GRCh38, GRCm38
Supplementary_files_format_and_content: tab-delimited text files include counts for each sample ([ENSG|ENSMUSG]\tCOUNT)
|
| |
|
| Submission date |
May 08, 2019 |
| Last update date |
Aug 30, 2019 |
| Contact name |
Garrett Thomas Graham |
| E-mail(s) |
gtg9@georgetown.edu
|
| Phone |
8148822017
|
| Organization name |
Georgetown University Medical Center
|
| Department |
Oncology
|
| Street address |
3970 Reservoir Rd NW
|
| City |
Washington |
| State/province |
DC |
| ZIP/Postal code |
20007 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE130903 |
Short and long-term effects of CDK4/6 inhibition on early stage breast cancer |
|
| Relations |
| BioSample |
SAMN11605092 |
| SRA |
SRX5807148 |
