|
| Status |
Public on Aug 08, 2023 |
| Title |
Mouse Lung tumor_KrasLA1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Lung primary tumors
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung primary tumors
strain: C57B6J
Sex: Male
genotype: KrasLA1/+
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 |
SAMN34072380 |
| SRA |
SRX19868731 |
