|
| Status |
Public on Mar 17, 2021 |
| Title |
KL84-Kras-Lkb1-NA |
| Sample type |
SRA |
| |
|
| Source name |
conditional activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with Lkb1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lung Tumor
genotype: (KrasG12DLkb1fl/fl)
background strain: C57BL/6
|
| Growth protocol |
The genetically engineered mouse model (GEMM) harboring a conditional activating mutation of endogenous Kras (KrasLSL-G12D/+) crossed with Lkb1 or p53 conditional knockout (Lkb1fl/fl or Trp53fl/fl) has been previously described. Briefly This KrasLSL-G12D strain carries a Lox-Stop-Lox (LSL) sequence followed by the KrasG12D point mutation allele commonly associated with human cancer. Trp53 exons 2-10 are flanked by loxP sites in this conditional targeted mutation. For Lkb1fl/fl mice, the transcript from the Lkb1 null allele eliminates exons 2–6, resulting in a translational frameshift. All the mice are crossed and confirmed with higher than 90% C57BL/6 genetic background by SNP analysis. CRE recombinase was induced through intranasal inhalation of 1x107 p.f.u. adeno-Cre (University of Iowa adenoviral core). The induced mice were evaluated by MRI imaging to quantify the lung tumor burden, and KP (KrasG12DTrp53fl/fl) and KL (KrasG12DLkb1fl/fl) lung tumor nodules were obtained and tumor cell lines were generated from these nodules ex vivo similar as previously reported.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with Qiagen RNeasy Mini Kit from fresh frozen tissue and quality checked by Agilent Bioanalyzer.
mRNA-Seq library made with Illumina TruSeq RNA Library Prep Kit v2 (Cat# RS-122-2001), 0.5ug of total RNAs was used for the construction of libraries according to the manufacturer’s protocol. Unique Dual indexes (TruSeq RNA UD Indexes, Cat# 20022371) were used for each library instead single index. cDNA libraries were sequenced using an Illumina HiSeq2500, producing 2x50bp paired-end reads with multiplexing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
KL.GEMMnodule
|
| Data processing |
mRNA-Seq libraries were aligned to the mouse mm10 using the STAR aligner algorithm. Resulting BAM files were sorted and indexed using Samtools and QC was performed using Picard. Tran-script read counts were determined was performed using Salmon
Gene counts were normalized using upper-quartile normalization, log transformed and median centred to construct the normalized gene matrix
Genome_build: mm10
Supplementary_files_format_and_content: fastqs, raw and normalized data matrix
|
| |
|
| Submission date |
Sep 13, 2019 |
| Last update date |
Mar 17, 2021 |
| Contact name |
Charles M. Perou |
| E-mail(s) |
cperou@med.unc.edu
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center
|
| Street address |
12-044 Lineberger Comprehensive Cancer Center CB# 7295
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599-7264 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE137396 |
Characterization of transcriptional analysis of LKB1 mutant lung nodules |
|
| Relations |
| BioSample |
SAMN12742317 |
| SRA |
SRX6843188 |
