|
| Status |
Public on Jul 07, 2022 |
| Title |
At_4 |
| Sample type |
SRA |
| |
|
| Source name |
Lung adenocarcinoma
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung adenocarcinoma
genotype: KrasLSL-G12D/+; Trp53LSL-R172H/+
treatment: Acidovorax temperans
|
| Treatment protocol |
Mice aged 5-9 w.o. were instilled with Adcre to activate the mutant Kras/p53 alleles. PBS (sham) or A. temperans were first instilled two weeks later and bacterial doses were repeated biweekly an additional five times, with mice sacrificed for tissue collection 14 weeks post-Adcre.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lung tissues were perfused then collected and dissected and then digested using the Mouse Tumor Dissociation Kit (Miltenyi Biotec) according to the manufacturer's instructions. Tissue digests were filtered through a 40 µm strainer and RBCs were lysed prior to staining with PE-conjugated anti-CD45 antibody (BD, clone 104) and sorting on a BD FACSAria.
Single cells were droplet captured according to the manufacturer's protocol (10X Genomics Chromium 3' Dual Index v3.2).
Sequencing was performed on Illumina NovaSeq S2 with 10 bp indices i5 and i7, 28 bp R1, and 90 bp R2 length reads with a target depth of 50,000 reads per cell.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Data processing was performed using Seurat v4.1.0.
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
|
| |
|
| Submission date |
Jul 05, 2022 |
| Last update date |
Jul 07, 2022 |
| Contact name |
Joshua Stone |
| E-mail(s) |
josh.stone@nih.gov
|
| Organization name |
NIH
|
| Street address |
37 Convent Drive Room 3050
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE207477 |
Acidovorax temperans skews neutrophil maturation and polarizes Th17 cells to promote lung adenocarcinoma development |
|
| Relations |
| BioSample |
SAMN29501181 |
| SRA |
SRX16020876 |
