|
| Status |
Public on Nov 24, 2022 |
| Title |
E-301 + ICI |
| Sample type |
SRA |
| |
|
| Source name |
B16D5-HER2 tumor
|
| Organism |
Mus musculus |
| Characteristics |
tissue: B16D5-HER2 tumor
cell type: CD45+ cells
strain: C57BL/6
treatment: E-301 + ICI
|
| Treatment protocol |
Mice carrying established B16D5-Her2 tumors were treated every 2nd day and tumors harvested 7 days post initial treatment.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Tumors were resected, mechanically dissected and enzymatically digested. Following a gradient centrifugation, single-cell suspensions were sorted for viable CD45+ cells.
The Chromium Next GEM Single Cell 3' v3.1 kit was used and library construction was performed according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
3' mRNA Library
|
| Data processing |
Samples were demultiplexed and aligned using Cell Ranger 6.1 (10X Genomics) to genome build mm10 to obtain a raw read count matrix of barcodes corresponding to cells and features corresponding to detected genes.
Mapped read counts were analysed using Seurat v.4 and harmonized to remove biological replicate associated effects using harmony.
Assembly: mm10
Supplementary files format and content: Processed data are matrices with raw counts for features in sequenced cells (matrix.mtx). A list of cell barcodes and detected genes is also included for each sample (barcodes.tsv, features.tsv).
|
| |
|
| Submission date |
Jul 13, 2022 |
| Last update date |
Nov 24, 2022 |
| Contact name |
Immunometabolism Department |
| E-mail(s) |
jcurti29@jhmi.edu
|
| Organization name |
Johns Hopkins University
|
| Department |
Immunometabolism
|
| Street address |
1650 Orleans Street
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21287 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE208133 |
Targeting cancer glycosylation repolarizes tumor-associated macrophages allowing effective immune checkpoint blockade |
|
| Relations |
| BioSample |
SAMN29716867 |
| SRA |
SRX16202218 |
