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Status |
Public on Sep 23, 2020 |
Title |
76_SMG_KO_S30 |
Sample type |
SRA |
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|
Source name |
Mouse Submandilar Salivary Gland
|
Organism |
Mus musculus |
Characteristics |
age: Adult (12wk) tissue: Salivary Gland genotype/variation: p63 Knockout 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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina MiSeq |
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|
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.
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|
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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 |
SAMN14096587 |
SRA |
SRX7719470 |