|Public on Nov 22, 2016
|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
|the mice were 8-12 weeks old
|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.
|Illumina NextSeq 500
processed data file: low_input_RNA_d30_fpkm.txt
|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
|Jun 14, 2016
|Last update date
|Oct 11, 2021
|Cedars Sinai Medical Center
|8687 Melrose Ave, PDC B230
|p53 is a critical regulator of airway epithelial progenitor cell homeostasis.