|
| Status |
Public on Jun 19, 2019 |
| Title |
Pal_T |
| Sample type |
SRA |
| |
|
| Source name |
CDK4/6 inhibitor Palbociclib treated tumor CD45- cells
|
| Organism |
Mus musculus |
| Characteristics |
mouse strain: FVB/N
genotype: MMTV-neu202Mul
tissue: spontaneous mammary tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh mammary tumors were enzymatically digested. Cells for single cell RNA-seq were prepared by density centrifugation using Ficoll-Paque media (GE Healthcare) followed by magnetic-activated cell sorting (Miltenyi) based separation or enrichment.
RNA libraries were prepared for sequencing using standard Illumina protocols for Nextera XT DNA sample prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The raw Drop-seq data were processed and aligned (STAR aligner) by following the standard Drop-seq pipeline (http://mccarrolllab.com/dropseq/). Read 1 contained both a cell barcode and a molecular barcode (UMI); read 2 was aligned to the reference genome (mm10). The cell barcode was extracted from bases 1-12, the UMI was extracted from bases 13-20.
Tumor cells (CD45- cells) pooled from three or four tumors. For tumor infiltrating leukocyte (TIL) and MDSC samples: Rep1 and Rep2 represented biological repeat. The last three number in name of raw files (001 and 002) for some TIL samples as indicated, represented technical repeat.
After generating the digital gene expression data matrix, the Seurat R package (Satija, 2015) was used to perform data normalization, dimension reduction, clustering and differential expression analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include UMI values for each sample/gene
|
| |
|
| Submission date |
Nov 08, 2018 |
| Last update date |
Jun 19, 2019 |
| Contact name |
Qingfei Wang |
| E-mail(s) |
qwang9@nd.edu
|
| Organization name |
University of Notre Dame
|
| Department |
Harper Cancer Research Institute
|
| Lab |
Zhang Lab
|
| Street address |
1234 N Notre Dame Ave, Harper Hall A121
|
| City |
South Bend |
| State/province |
IN |
| ZIP/Postal code |
46617 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE122336 |
Single-cell profiling guided combinatorial immunotherapy for breast cancer resistance to Her2/neu and CDK4/6 targeted therapy |
|
| Relations |
| BioSample |
SAMN10396992 |
| SRA |
SRX4997100 |
