NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM6288361 Query DataSets for GSM6288361
Status Public on Jul 07, 2022
Title At_3
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 SAMN29501182
SRA SRX16020875

Supplementary file Size Download File type/resource
GSM6288361_A3_filtered_feature_bc_matrix.tar.gz 51.6 Mb (ftp)(http) TAR
GSM6288361_A3_raw_feature_bc_matrix.tar.gz 110.8 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap