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Sample GSM7146634 Query DataSets for GSM7146634
Status Public on Aug 08, 2023
Title Mouse Lung tumor_KrasLA1;DicerS2D_rep2
Sample type SRA
 
Source name Lung primary tumors
Organism Mus musculus
Characteristics tissue: Lung primary tumors
strain: C57B6J
Sex: Male
genotype: KrasLA1/+;Dicer1S2D/+
age in_weeks: 39w
Treatment protocol No treatment
Growth protocol Heterozygous phosphomimetic Dicer1 (Dicer1S2D/+) animals were crossed to heterozygous Kras G12D (KrasLA1/+) animals to generate a cohort of Dicer1S2D/+, KrasLA1/+ and KrasLA1/+;Dicer1S2D/+ animals. Mice were euthanized at 39weeks of age for tissue collection.
Extracted molecule total RNA
Extraction protocol Briefly, 39 weeks old mice were anesthetized using Avertin (Sigma, T4802), right heart ventricle was perfused with 1x PBS without calcium and magnesium (ThermoFisher, #100100023). Lungs were removed from the mouse and placed in Liebovitz media (Gibco, #21083-023). Lung tumors were identified and collected under the dissecting microscope. Tumors were minced with forceps and digested in the Liebovitz media with 2 mg/mL collagenase type I (Worthington CLS-1, LS004197), 0.5 mg/mL DNase I (Worthington D LS002007) and 2 mg/mL elastase (Worthington ESL LS002294) for 30 min at 37oC. Digestion was stopped with 20% Fetal bovine serum (FBS, Invitrogen 10082- 139). Cells were filtered using a 70 µm cell strainer (Falcon, 352350) on ice and transferred to a 2mL tube. Red blood cells were lysed using Red blood cells lysis buffer (Miltenyl Biotec 130-094-183), and the lysate centrifuged for 1 minute at 5000rpm. Supernatant was removed and cells in the pellet were washed twice with 1mL of ice-cold 1X Leibovitz plus 10% FBS. The cellular suspension was then filtered with a 40 µm cell strainer (Falcon #352340), centrifuged and cells resuspended in ice-cold 1X Leibovitz plus 10% FBS. Cell viability was evaluated using Trypan blue and counted with a hemocytometer. Samples with more than 70% of viable cells were submitted for scRNA-seq
After cell dissociation and counting, samples were centrifuged and re-suspended in 1X PBS with 0.04% BSA for single cell suspensions and processed for Chromium Single Cells Gene Expression Solution Platform (10x Chromium) with 3’v3 Library following manufacture instructions.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 10x Genomics
Data processing FASTQC files were processed using Cellranger v3.1.0 software
Clustering and cell population annotations were performed in R studio following Seurat algorithm.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
 
Submission date Apr 04, 2023
Last update date Aug 08, 2023
Contact name Raisa Reyes-Castro
E-mail(s) RAReyes2@mdanderson.org
Organization name UT Health MD Anderson Cancer Center
Department Genetics
Lab Swathi Arur
Street address 6767 Bertner Ave
City Houston
State/province Texas
ZIP/Postal code 77030
Country USA
 
Platform ID GPL24247
Series (2)
GSE228965 Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas [scRNA-seq]
GSE228968 Phosphorylated nuclear DICER1 promotes open chromatin state and gastric cell fate in lung adenocarcinomas
Relations
BioSample SAMN34072378
SRA SRX19868733

Supplementary file Size Download File type/resource
GSM7146634_SC142_4_T3_barcodes.tsv.gz 53.5 Kb (ftp)(http) TSV
GSM7146634_SC142_4_T3_features.tsv.gz 272.8 Kb (ftp)(http) TSV
GSM7146634_SC142_4_T3_matrix.mtx.gz 39.9 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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