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Sample GSM2671311 Query DataSets for GSM2671311
Status Public on May 31, 2018
Title siControl_High_Ca_3
Sample type SRA
 
Source name BALB/c neonatal mouse keratinocyte culture
Organism Mus musculus
Characteristics treatment: siControl
batch: batch2
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 SAMN07249187
SRA SRX2924798

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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