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GSE35077
Mus musculus
26 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The goal of this experiment was to define gene expression patterns of thirteen mouse retinal neuron subsets, labeled by expression of fluorescent proteins in transgenic mice.
Publication Title
MEGF10 and MEGF11 mediate homotypic interactions required for mosaic spacing of retinal neurons.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
We have shown that removal of Lkb1 in chondorcytes results in enchondroma-like structure in postnatal mouse long bones. To furhter understand the role of Lkb1 in this process, we performed microarrrays to compare the transcriptional profile between control and conditional Lkb1 mutant (Col2a1-Cre; Lkb1c/c) chondrocytes.
Publication Title
Lkb1/Stk11 regulation of mTOR signaling controls the transition of chondrocyte fates and suppresses skeletal tumor formation.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The goal of this experiment was to define gene expression patterns of two mouse retinal neuron subsets that express the Thy1-mitoCFP-P (MP) transgene.
Publication Title
Neurod6 expression defines new retinal amacrine cell subtypes and regulates their fate.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Satb1 Regulates Contactin 5 to Pattern Dendrites of a Mammalian Retinal Ganglion Cell.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The goal of this experiment was to define gene expression patterns of two mouse retinal ganglion cell subsets, labeled by expression of fluorescent proteins in Hb9-GFP and Drd4-GFP mice, all retinal ganglion cells labeled by anti-Thy1 antibody staining.
Publication Title
Satb1 Regulates Contactin 5 to Pattern Dendrites of a Mammalian Retinal Ganglion Cell.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
Illumina HiSeq 4000
Description
At least 30 types of retinal ganglion cell (RGC) send distinct messages through the optic nerve to the brain. Strategies for promoting regeneration of RGC axons following injury act on only some of these types. Here we tested the hypothesis that over-expressing developmentally important transcription factors in adult RGCs could reprogram them to a “youthful” growth-competent state and promote regeneration of other types. From a screen of transcription factors expressed by developing RGCs, we found one, Sox11, that induced substantial axon regeneration. Transcriptome profiling confirmed that Sox11 activates genes involved in cytoskeletal remodeling and axon growth. Remarkably, alpha-RGCs, which preferentially regenerate following treatments such as PTEN deletion, were killed by Sox 11. Thus, Sox 11 promotes regeneration of non-alpha RGCs, which are refractory to PTEN. We conclude that Sox11 can reprogram adult RGCs to a growth-competent state and that different growth-promoting interventions act on distinct neuronal types. Overall design: We compared transcriptomes of retinal ganglion cells between AAV-Control retinas, and retinas treated with AAV-Sox11 overexpression. We then performed optic nerve crush, and 3 days later purified RGCs using FACS. RGCs were marked with Thy1-PE-Cy7 antibody and with live/dead cell staining. We performed sample preparations in full triplicate, and in each replicate we always performed Control and Sox11 on the same day, in alternating order.
Publication Title
Sox11 Expression Promotes Regeneration of Some Retinal Ganglion Cell Types but Kills Others.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 381 Downloadable Samples
- Illumina HiSeq 2500
Description
Four Kcng4-cre;stop-YFP mouse retinas from two mice were dissected, dissociated and FACS sorted, and single cell RNA-seq libraries were generated for 384 single cells using Smart-seq2. Aligned bam files are generated for 383 samples as one failed to align. Overall design: Four mouse retinas (labeled 1la, 1Ra, and 2la, 2Ra respective from the two mice) were used, and 96 single cells from each were processed using Smart-seq2. Total 384 cells Smart-seq2 analysis of P17 FACS sorted retinal cells from the Kcng4-cre;stop-YFP mice (Kcng4tm1.1(cre)Jrs mice [Duan et al., Cell 158, 793-807, 2015] crossed to the cre-dependent reporter Thy1-stop-YFP Line#1 [Buffelli et al., Nature 424, 430-434, 2003])
Publication Title
Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 2 Downloadable Samples
- Illumina HiSeq 2500
Description
15,000 GFP+ cells were collected from two replicates of the Htr3a GFP line into RNAlater (ThermoFisher, AM7024). RNA was purified and bulk RNA-seq was performed using the Ovation RNA-seq system V2 (Nugen, 7102-32) Overall design: Bulk RNA-seq analysis of Type 5 retinal bipolar cells (2 biological replicates)
Publication Title
Comprehensive Classification of Retinal Bipolar Neurons by Single-Cell Transcriptomics.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 192 Downloadable Samples
- NextSeq500
Description
A cell supsension containing an equal mix of HEK and 3T3 cells was used in the Fluidigm C1 Overall design: Suspensions of 3T3 and HEK cells were diluted down to a concentration of 250,000 per mL and mixed 1:1, then loaded onto two medium C1 cell capture chips.
Publication Title
Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 12 Downloadable Samples
- Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
Expression data from rat with anti-glomerular basement membrane nephritis (anti-GBM). We used microarrays to analyze the transcriptome of kidney from anti-GBM model rat with or without drug treatment
Publication Title
Effects of a Tricaprylin Emulsion on Anti-glomerular Basement Membrane Glomerulonephritis in Rats: In Vivo and in Silico Studies.
Sample Metadata Fields
Specimen part
View Samples