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Data Set Group2: 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
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.


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:


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


  • 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:

CITG Web services initiated January, 1994 as Portable Dictionary of the Mouse Genome; June 15, 2001 as WebQTL; and Jan 5, 2005 as GeneNetwork. This site is currently operated by Rob Williams, Pjotr Prins, Zachary Sloan, Arthur Centeno. Design and code by Pjotr Prins, Zach Sloan, Arthur Centeno, Danny Arends, Christian Fischer, Sam Ockman, Lei Yan, Xiaodong Zhou, Christian Fernandez, Ning Liu, Rudi Alberts, Elissa Chesler, Sujoy Roy, Evan G. Williams, Alexander G. Williams, Kenneth Manly, Jintao Wang, and Robert W. Williams, colleagues. Python Powered Registered with Nif
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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