|
| Status |
Public on May 07, 2023 |
| Title |
20230111_30102627890622-01_Sample04_04 |
| Sample type |
RNA |
| |
|
| Source name |
Sorted Monocytes_CRT
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
cell type: CD8+ T cells
treatment: conformal radiotherapy
|
| Treatment protocol |
Tumors were digested with collogenase and Dnase into a single cell suspension. Cells were stained with primary antibody, enriched with CD45-biotin and anti-biotin beads, and sorted for CD8+ T cells
|
| Growth protocol |
MC38 tumor cells were implanted into C57BL/6J mice and treated with radiationtherapy (20Gy) once the tumor reached 40-100 mm3.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed and resuspended in 1/3 RNeasy Lysis Buffer RLT (Qiagen) at a concentration of 1,000-5,000 cells/μL. Samples were analyzed on the NanoSting nCounter® Mouse NanoString nCounter® Mouse Myeloid Innate Immunity V2 Panel Standard Platform according to the manufacturer’s instructions.
|
| Label |
n/a
|
| Label protocol |
N/A
|
| |
|
| Hybridization protocol |
N/A
|
| Scan protocol |
N/A
|
| Description |
Sorted CD8+ T cells_CRT sequenced by NanoSTRING and counts were normalized via ROSALIND software
|
| Data processing |
Data was analyzed by ROSALIND® with a HyperScale architecture developed by ROSALIND, Inc. (San Diego, CA). Normalization, fold changes and p-values were calculated using criteria provided by NanoSTRING ROSALIND® follows the nCounter® Advanced Analysis protocol of dividing counts within a lane by the geometric mean of the normalizer probes from the same lane. Housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library. Fold changes and pValues are calculated using the fast method as described in the nCounter® Advanced Analysis 2.0 User Manual
|
| |
|
| Submission date |
Jan 20, 2023 |
| Last update date |
May 09, 2023 |
| Contact name |
Juliana Idoyaga |
| E-mail(s) |
jidoyaga@stanford.edu
|
| Phone |
6504980717
|
| Organization name |
Stanford University
|
| Department |
Microbiology and Immunology
|
| Street address |
299 Campus drive, 3RD FLOOR RM D330 & D345
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL25266 |
| Series (1) |
| GSE223400 |
NanoSTRING analysis of sorted monocytes/monoACT cells following radiotherapy |
|
