|
| Status |
Public on Feb 01, 2018 |
| Title |
IMOK_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Immortalised Mouse Oral Keratinocyte
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Immortalised Mouse Oral Keratinocyte
growth condition: IMOK media
passage: Early
|
| Treatment protocol |
N/A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from mouse submandibular salivary gland epithelial cells using the Direct-zol RNA Mini-Prep kit.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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 (v1.12.4) was used to normalize the read counts and derive FPKM values and TPM values were calculated by dividing the FPKM value of each gene by the total FPKM values in the sample.
Genome_build: mm9
Supplementary_files_format_and_content: featureCounts output containing gene-level read count summaries for each RNA-Seq sample
|
| |
|
| Submission date |
Apr 26, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Rose-Anne Romano |
| E-mail(s) |
rromano2@buffalo.edu
|
| Organization name |
State University of New York at Buffalo
|
| Department |
Oral Biology
|
| Lab |
210 Foster
|
| Street address |
3435 Main Street
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14214 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE98250 |
Functional characterization and genomic studies of a novel murine submandibular gland epithelial cell line. |
|
| Relations |
| BioSample |
SAMN06837795 |
| SRA |
SRX2766159 |
