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| Status |
Public on Dec 01, 2018 |
| Title |
Stroma_ctrl_untx_4 |
| Sample type |
SRA |
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| Source name |
Stroma Unwounded untreated
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| Organism |
Mus musculus |
| Characteristics |
tissue: cornea
tissue compartment: Stroma
wound status: Unwounded
treatment: untreated
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| 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
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| Submission date |
Jun 05, 2018 |
| Last update date |
Dec 01, 2018 |
| Contact name |
Maria Irene Morasso |
| E-mail(s) |
morassom@mail.nih.gov
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| Phone |
3014357842
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| Organization name |
NIAMS NIH
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| Lab |
Laboratory of Skin Biology
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| Street address |
Bldg 50
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| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL21493 |
| Series (1) |
| GSE115355 |
Molecular basis of mitomycin C enhanced corneal sensory nerve repair |
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| Relations |
| BioSample |
SAMN09369099 |
| SRA |
SRX4168177 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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