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Sample GSM2200016 Query DataSets for GSM2200016
Status Public on Nov 22, 2016
Title p53_knock_out (d30_p53_10)
Sample type SRA
Source name lung_p53_knock_out
Organism Mus musculus
Characteristics genotype: p53-/-
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_p53_10
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.
BioSample SAMN05247031
SRA SRX1844101

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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