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Sample GSM4310371 Query DataSets for GSM4310371
Status Public on Sep 23, 2020
Title 6593_WT_SMG_S19
Sample type SRA
 
Source name Mouse Submandilar Salivary Gland
Organism Mus musculus
Characteristics age: Adult (12wk)
tissue: Salivary Gland
genotype/variation: p63 WildType mouse
Extracted molecule total RNA
Extraction protocol Mouse submandibular salivary gland epithelial cells were isolated from adult wildtype and p63 knockout mice and RNA was extracted using the Direct-zol RNA Mini-Prep kit.
Library preparation was carried out using the Illumina TruSeq RNA Sample Prep Kit protocol. 1 ug of total RNA from each sample was used in the the construction of sequencing libraries.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina MiSeq
 
Description TPM values were generated by normalizing raw counts for both library size and gene length.
Data processing Reads were mapped to the Mus musculus genome (mm9 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm9 build were quantified with featureCounts (v1.5.1) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.20.0) was used to normalize the read counts, and TPM values were calculated by normalising read counts were further normalised by gene length and total counts to generate Transcript Per Million (TPM) values.
Genome_build: mm9
Supplementary_files_format_and_content: TPM values were generated by normalizing raw counts for both library size and gene length.
 
Submission date Feb 13, 2020
Last update date Sep 23, 2020
Contact name Jonathan E Bard
E-mail(s) jbard@buffalo.edu
Organization name University at Buffalo
Department Genomics and Bioinformatics Core
Street address 701 Ellicott Street
City Buffalo
State/province New York
ZIP/Postal code 14203
Country USA
 
Platform ID GPL16417
Series (2)
GSE145266 p63 Maintains the Proliferative Potential of Salivary Gland Stem/Progenitor Cells by Regulating Follistatin, a Key Mediator of TGF-b/Activin Signaling [RNA-seq]
GSE145268 p63 Maintains the Proliferative Potential of Salivary Gland Stem/Progenitor Cells by Regulating Follistatin, a Key Mediator of TGF-b/Activin Signaling
Relations
BioSample SAMN14096585
SRA SRX7719472

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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