|
| Status |
Public on May 18, 2017 |
| Title |
MK2_RNA_Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Mouse keratinocyte cell-line 2
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MK2
cell type: keratinocyte
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from mouse keratinocyte cells (MK1 and MK2) 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 (mm10 build) with TopHat2 (v2.0.13),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the UCSC mm10 build were quantified with featureCounts (v1.5.0) , which disregarded any read/read pair that aligned to more than one location, or more than one gene at a single location.
DESeq2 (v1.10.1) was used to normalize the read counts and derive FPKM values.
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts output containing gene-level read count summaries for each RNA-Seq sample
|
| |
|
| Submission date |
Sep 13, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Satrajit Sinha |
| E-mail(s) |
ssinha2@buffalo.edu
|
| Phone |
716-881-7994
|
| Organization name |
State University of New York at Buffalo
|
| Department |
Department of Biochemistry
|
| Street address |
701 Ellicott Street
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE86901 |
Evolutionary re-wiring of p63 regulatory landscape has both epigenetic and transcriptomic implications and is the underlying cause for epidermal differences between mouse and human [RNA-seq] |
| GSE86902 |
Evolutionary re-wiring of p63 regulatory landscape has both epigenetic and transcriptomic implications and is the underlying cause for epidermal differences between mouse and human |
|
| Relations |
| BioSample |
SAMN05770695 |
| SRA |
SRX2162786 |
