|
| Status |
Public on May 31, 2018 |
| Title |
C_H2 |
| Sample type |
SRA |
| |
|
| Source name |
BALB/c neonatal mouse keratinocyte culture
|
| Organism |
Mus musculus |
| Characteristics |
treatment: siControl
batch: batch1
strain: BALB/c
|
| Treatment protocol |
A total of 1 million cells were seeded in each well of 6 well plates. 24 hours after seeding, the siRNA mix (Opti-Mem serum free media (GIBCO), 75pmol of siRNA (Dharmacon) and HiPerfect transfection reagent (Qiagen)) was added to cells. For SBSN, the siRNA used were Dharmacon, SMARTpool; siGENOME Sbsn siRNA M-054578-01-0005 and Control (mouse) SMARTpool; siGENOME Non-Targeting siRNA Pool #1. Each condition was done in triplicates. To induce keratinocyte differentiation, a final concentration of 0.12mM Ca++ was used. RNA was harvested 48hs after siRNA transfection.
|
| Growth protocol |
Primary murine keratinocytes were cultured in supplemented minimal essential medium (Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA) with 8% fetal bovine serum (FBS, Atlanta Biologicals, Flowery Branch, GA, USA) and 1% antibiotic (Penicillin Streptomycin Amphotericin B, Sigma), with Ca++ concentration of 0.05mM.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from cells was extracted using RNeasy kit (Qiagen) according to the manufacturer’s instructions.
100 ng were used to prepare the libraries utilizing a Neoprep Library kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The raw reads were done by STAR.
Normalization and differential gene analysis were done using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count table
|
| |
|
| Submission date |
Jun 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Maria I. Morasso |
| E-mail(s) |
morassom@mail.nih.gov
|
| Phone |
301-402-2888
|
| Organization name |
National Institutes of Health
|
| Department |
National Institute for Arthritis and Musculoskeletal and Skin Diseases
|
| Lab |
Laboratory of Skin Biology
|
| Street address |
Building 50, Room 1525 10 Center Drive
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE100100 |
A data mining paradigm for identifying key factors in biological processes using gene expression data |
|
| Relations |
| BioSample |
SAMN07249190 |
| SRA |
SRX2924795 |
