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Series GSE4051 Query DataSets for GSE4051
Status Public on Feb 28, 2006
Title Targeting of GFP to new-born rods by Nrl promoter and temporal expression profiling of flow-sorted photoreceptors
Organism Mus musculus
Experiment type Expression profiling by array
Summary Purpose: To investigate the gene regulatory networks during photoreceptor differentiation.
Special aims: To generate gene expression profiles of purified photoreceptors at distinct developmental stages and from different genetic backgrounds.
Background: Rod photoreceptor genesis spans a broad temporal window during retinal development. It starts as early as E12.5 and peaks at P0-P2. At E16.5, there are some early born rods but the peak of rod genesis does not occur. At P2, the majority of rod photoreceptors are born. At P6, rod specific structural/functional genes begin to express. At P10, Outer segments morphogenesis is taking place. At 4 weeks, retinal development is complete and retina is functional. Nrl is a rod specific transcription factor and one of the earliest markers of rod photoreceptors. Nrl promoter drives the expression of GFP exclusively to rod photoreceptors shortly after they exit cell cycle. In the Nrl-knockout background, the expression of GFP is detected in S-opsin positive cells, which suggested a cell fate transformation from rods to cones in the absence of Nrl.
Design: GFP positive photoreceptors from the WT-Gfp or Nrl-knockout-Gfp retina were enriched (purified) by FACS at five distinct developmental stages (E16, P2, P6, P10, and 4 weeks). Total RNA was extracted by Trizol reagent. Around 50 ng of total RNA was used for linear amplification and biotin labeling followed Nugen kit protocol. Fragmented cDNA was hybridized on Affymetrix mouse genomic expression array 430 2.0 and then scanned with the standard protocol. Four replicates were performed for each time point.
Conclusion: By comparing the gene expression profiles from different developmental stages, we can obtain novel insights into molecular events underlying photoreceptor differentiation.
Keywords: Transcription factor, development, photoreceptor, retina, neuron, differentiation, gene regulation, microarray, gene profiling, cell type comparison
 
Overall design Postmitotic rod precursors and mature rod photoreceptors are tagged by GFP under the control of an Nrl promoter in the wild type background (Wt-Gfp mice). When cross-bred into the Nrl-knockout background (Nrl-ko-Gfp mice), the transformed “S-cones” are tagged by GFP. GFP positive photoreceptors from the Wt-Gfp or Nrl-ko-Gfp retina were enriched (purified) by FACS at five distinct developmental stages (E16, P2, P6, P10, and 4 weeks). Total RNA was extracted by Trizol regent and around 50 ng of total RNA was used for linear amplification and biotin labeling following Nugene kit protocol. Fragmented cDNA was hybridized on Affymetrix mouse genomic expression array 430 2.0 and then scanned with the standard protocol. Four replicates were performed for each time point.
 
Contributor(s) Akimoto M, Cheng H, Zhu D, Brzezinski JA, Khanna R, Filippova E, CT Oh E, Jing Y, Linares J, Brooks M, Zareparsi S, Mears AJ, Hero A, Glaser T, Swaroop A
Citation(s) 16505381
Submission date Jan 17, 2006
Last update date Feb 11, 2019
Contact name Swaroop Anand
E-mail(s) swaroop@umich.edu
Phone 734-615 2246
URL http://www.umich.edu/~retina
Organization name University of Michigan
Department Ophthalmology & Visual Sciences
Street address 1000 Wall St.
City Ann Arbor
State/province MI
ZIP/Postal code 48105
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (39)
GSM92610 Nrl-ko-Gfp 4 weeks retina replicate 1
GSM92611 Nrl-ko-Gfp 4 weeks replicate 2
GSM92612 Nrl-ko-Gfp 4 weeks replicate 3
Relations
BioProject PRJNA95193

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE4051_Nrl-ko-Gfp-PAdetectioncalls.txt 1.5 Mb (ftp)(http) TXT
GSE4051_RAW.tar 253.3 Mb (http)(custom) TAR (of CEL)
GSE4051_wt-Gfp-PAdetectioncalls.txt 1.5 Mb (ftp)(http) TXT
Raw data provided as supplementary file

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