|
| Status |
Public on Nov 22, 2016 |
| Title |
wild_type (d30_wt_1) |
| Sample type |
SRA |
| |
|
| Source name |
lung_wild_type
|
| Organism |
Mus musculus |
| Characteristics |
genotype: wild type
tissue: lung
|
| Treatment protocol |
GFP+, EpCAM+,CD31/34/45-,7AAD- cells were sorted from either Scgb1a1-CreERTM; Rosa26-mT/mG; p53+/+ or Scgb1a1-CreERTM; Rosa26-mT/mG; p53flox/flox mice at 70 days after tamoxifen exposure
|
| Growth protocol |
the mice were 8-12 weeks old
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Micro Kit (Quiagen)
Total RNA was quantified using both the NanoDrop to assess sample contamination by proteins or carryover reagents from RNA isolation, and the Qubit fluorometer (Invitrogen). Samples were then qualified using the Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) that analyzes the integrity of the total RNA by measuring the ratio between the 18S and 28S ribosomal peaks. Libraries were constructed using SMARTer Ultra Low Input RNA v3 kit (Clontech), indexed using Nextera indices (Illumina). Final libraries were again quantitated with the Qubit fluorometer and checked for size via the Fragment Analyzer. Libraries were diluted to 4nM and pooled in equal volumes for denaturation, hybridization, and sequencing on an Illumina NextSeq 500 (Illumina) with single end 75bp sequencing chemistry.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
d30_wt_1
processed data file: low_input_RNA_d30_fpkm.txt
|
| Data processing |
We used the Basespace RNA-Seq Alignment app, which uses the TopHat (Bowtie2) aligner. We then used Cufflinks Assembly and DE to get the significantly differentially expressed genes between wt and p53 samples
Genome_build: mm10 from Basespace
Supplementary_files_format_and_content: [.txt] table includes fpkm values for each Sample calculated by tophat
|
| |
|
| Submission date |
Jun 14, 2016 |
| Last update date |
Oct 11, 2021 |
| Contact name |
AGCT Core |
| Organization name |
Cedars Sinai Medical Center
|
| Department |
BMS
|
| Street address |
8687 Melrose Ave, PDC B230
|
| City |
West Hollywood |
| State/province |
CA |
| ZIP/Postal code |
90069 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE78045 |
p53 is a critical regulator of airway epithelial progenitor cell homeostasis. |
|
| Relations |
| BioSample |
SAMN05247026 |
| SRA |
SRX1844096 |
