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Sample GSM3176489 Query DataSets for GSM3176489
Status Public on Dec 01, 2018
Title Epi_ctrl_MMC_3
Sample type SRA
 
Source name Epidermis Unwounded MMC
Organism Mus musculus
Characteristics tissue: cornea
tissue compartment: Epidermis
wound status: Unwounded
treatment: MMC
Extracted molecule polyA RNA
Extraction protocol For RNA-seq studies, epithelium was isolated from mouse corneas. After limbal to limbal debridement, eyes were removed, corneas dissected to yield clear stromal buttons. For both epithelium and stroma, 4 variables were tested (Control, Mitomycin C Control, Wound, Mitomycin C Wound). RNA was extracted using Arcturus Picopure RNA isolation kit (Applied Biosystems).
cDNA libraries were generated using NEBnext and NuGen kits. Sequencing was performed on the HiSeq3000
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing BCL Conversion and Demultiplex bcl2fastq
Map to mm10 using Tophat 2.1.0
Calculate RPKM using Partek GS 6.6
ANOVA comparison using Partek GS 6.6
Genome_build: mm10
Supplementary_files_format_and_content: Excel, RPKM and ANOVA results
 
Submission date Jun 05, 2018
Last update date Dec 01, 2018
Contact name Maria Irene Morasso
E-mail(s) morassom@mail.nih.gov
Phone 3014357842
Organization name NIAMS NIH
Lab Laboratory of Skin Biology
Street address Bldg 50
City Bethesda
State/province Maryland
ZIP/Postal code 20892
Country USA
 
Platform ID GPL21493
Series (1)
GSE115355 Molecular basis of mitomycin C enhanced corneal sensory nerve repair
Relations
BioSample SAMN09369122
SRA SRX4168164

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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