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Series GSE222901 Query DataSets for GSE222901
Status Public on Feb 16, 2024
Title Single-cell analyis of tobacco-associated lung adenocarcinoma development
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Understanding cellular processes underlying early lung adenocarcinoma (LUAD) development is needed to devise intervention strategies. Here, we performed single-cell RNA sequencing (scRNA-seq) of mouse lungs from Gprc5a-/- mice during lung tumor development. We coupled scRNA-seq analysis with spatial transcriptomics of tumor-bearing lungs.
 
Overall design scRNA-seq profiling was performed on lungs from Gprc5a-/- mice treated with nicotine-derived nitrosamine ketone (NNK) or saline at the end of exposure (EOE, timepoint at which lungs are still clear of lesions) and at 7 months post-exposure, the time point of Kras-mutant LUAD onset in all mice (n = 4 mice per group and time point). We also performed scRNA-seq of GFP+ and GFP- fractions of lungs from Gprc5a-/- mice carrying alveolar type II reporter (Gprc5a-/-; SftpcCreER/+; RosaSun1GFP/+) at three months post-exposure to saline of NNK (n = 2 mice per group). scRNA-seq was performed using the 10X Genomics platform. Spatial transcriptomics of 3 tumor-bearing lung tissues from Gprc5a-/- mice at 7 months post-exposure to NNK was performed using the Visium platform from 10X Genomics to further characterize and validate scRNA-seq findings in a spatial context.
 
Contributor(s) Kadara H, Han G
Citation(s) 38418883
Submission date Jan 14, 2023
Last update date Apr 02, 2024
Contact name Humam Kadara
Organization name University of Texas MD Anderson Cancer Center
Street address 2130 W. Holcombe Blvd
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (27)
GSM6934986 Lungs from Gprc5a-/- mouse 1 at 7 months post-NNK [KOK7_45]
GSM6934987 Lungs from Gprc5a-/- mouse 2 at 7 months post-NNK [KOK7_46]
GSM6934988 Lungs from Gprc5a-/- mouse 3 at 7 months post-NNK [KOK7_47]
Relations
BioProject PRJNA923805

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Supplementary file Size Download File type/resource
GSE222901_RAW.tar 1.5 Gb (http)(custom) TAR (of MTX, TSV)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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