|
| Status |
Public on Jul 12, 2024 |
| Title |
8Gy+ICI |
| Sample type |
SRA |
| |
|
| Source name |
solid tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: solid tumors
cell type: tumor-infiltrating CD45+ cells
treatment: 8 Gy external beam radiation therapy+Immune checkpoint inhibitors
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumors were dissected from mice, minced, and digested using the Miltenyi Biotec tumor dissociation kit. Cells were strained through a 70 µm filter and washed with FACS buffer. Red blood cells were lysed using ACK lysis buffer, washed again with FACS buffer, and strained through a 40 µm filter. Cells were then washed and stained for CD45+ FACS.
Sorted live CD45+ cells were loaded on a Chromium iX single cell instrument (10x Genomics) to generate single-cell beads in emulsion and scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits (v3). Cells were sequenced to greater than 50,000 reads per cell over two lanes.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
10x Genomics
|
| Data processing |
The demultiplexing, barcode processing, and gene counting was performed using 10x Genomics Cell Ranger software v6.1.2
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix file of filtered feature counts data
|
| |
|
| Submission date |
Jun 05, 2023 |
| Last update date |
Jul 12, 2024 |
| Contact name |
Zachary Scott Morris |
| E-mail(s) |
zmorris@humonc.wisc.edu
|
| Phone |
6082632603
|
| Organization name |
University of Wisconsin-Madison
|
| Department |
Human Oncology
|
| Street address |
1111 Highland Ave., WIMR Tower 1, Room 3131
|
| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE234159 |
Intratumoral radiation dose heterogeneity augments antitumor immunity in mice and primes responses to checkpoint blockade |
| GSE234161 |
Intratumoral radiation dose heterogeneity augments antitumor immunity in mice and primes responses to checkpoint blockade |
|
| Relations |
| BioSample |
SAMN35624278 |
| SRA |
SRX20594384 |
