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Data Set Group: JAX Retina (Apr18) RNA-Seq modify this page

Data Set: JAX Retina (Apr18) RNA-Seq log2-Z modify this page
GN Accession: GN847
GEO Series: GSE90654
Title: RNA-seq analysis of RNA from DBA/2J retinal ganglion cells
Organism: Mouse (Mus musculus, mm10)
Group: D2GM
Tissue: Retina mRNA
Dataset Status: Public
Platforms: Illumina ScriptSeq RNA-Seq v2
Normalization: RNA-seq
Contact Information
Pete Williams
The Jackson Laboratory
600 Main Street
Bar Harbor, Maine 04609 USA
Tel. 207-288-1472
pete.williams@jax.org
Website
Download datasets and supplementary data files

Specifics of this Data Set:

RNA-Seq log2 Z-Score

In general, the array data that we put in GeneNetwork has been logged and then z normalized, but instead of leaving the mean at 0 and the standard deviation of 1 unit, we shift up to a mean of 8 units and increase the spread by having an standard deviation of 2 units (what we call 2Z + 8 normalized data).  This removes negative values from the tables.



Summary:

RNA-seq analysis from young and pre-glaucomatous DBA/2J retinal ganglion cells and control (age and sex-matched, D2-Gpnmb+) retinal ganglion cells



About the cases used to generate this set of data:


About the tissue used to generate this set of data:


About the array platform:

GPL17021Illumina HiSeq 2500 (Mus musculus)



About data values and data processing:


Notes:


Experiment Type:

Retinal ganglion cell mRNA from 4 month (young) and 9 month (pre-glaucomatous) DBA/2J mice and age and sex-matched D2-Gpnmb+ controls



Contributor:


Citation:
  • Williams PA, Harder JM, Foxworth NE, Cochran KE et al. Vitamin B3 modulates mitochondrial vulnerability and prevents glaucoma in aged mice. Science 2017 Feb 17;355(6326):756-760. PMID: 28209901


Data source acknowledgment:


Study Id:
275
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GeneNetwork support from:
  • The UT Center for Integrative and Translational Genomics
  • NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
  • NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
  • NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
  • NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
  • NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
  • NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)
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