|
| Status |
Public on Nov 10, 2023 |
| Title |
Beta-glucan_2 |
| Sample type |
SRA |
| |
|
| Source name |
Orthotopic tumor (PDA.7940B tumor cells)
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Orthotopic tumor (PDA.7940B tumor cells)
cell type: Polyclonal KPC derived mouse pancreatic ductal adenocarcinoma
genotype: WT
treatment: Beta-glucan (1.2mg IV x1)
|
| Treatment protocol |
Mice were implanted with PDA.7940B tumor cells into the pancreas. Ten days later mice were left untreated or were treated with a single dose of beta-glucan (1.2mg/kg) intravenous, anti-CD40 (0.1 mg) intraperitoneal or the combination and eight days later necropsy was performed.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumors were minced with micro-dissecting scissors at 4°C in DMEM containing collagenase (1mg/mL, Sigma-Aldrich) and DNase (150 U/mL, Sigma) and incubated at 37°C for 45 minutes with intermittent agitation. Tissues were filtered through a 70-um nylon strainer (Corning). Cells were then incubated in ACK lysing buffer (Life Technologies) for 5 minutes, washed with DMEM and filtered through a 40-um strainer and dead cells were removed by magnetic bead sorting per the manufacturer's protocol (Miltenyi).
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3.1 per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BG2
|
| Data processing |
Data was processed using the Cell Ranger pipeline (10x Genomics, v.6.1.2) for demultiplexing and alignment of sequencing reads to the mm10 transcriptome and creation of feature-barcode matrices.
Assembly: mm10
Supplementary files format and content: tar archives include barcodes.tsv, features.tsv, matrix.mtx, and filtered_feature_bc_matrix.h5 Cell Ranger pipeline outputs.
|
| |
|
| Submission date |
May 22, 2023 |
| Last update date |
Nov 10, 2023 |
| Contact name |
Max M Wattenberg |
| E-mail(s) |
max.wattenberg@pennmedicine.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Lab |
Beatty
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| State/province |
PENNSYLVANIA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE233171 |
Cancer immunotherapy via synergistic co-activation of myeloid cells [scRNA-seq] |
| GSE233175 |
Cancer immunotherapy via synergistic co-activation of myeloid cells |
|
| Relations |
| BioSample |
SAMN35312064 |
| SRA |
SRX20466714 |
