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SRP100444
Mus musculus
3 Downloadable Samples
NextSeq 500
Description
We report single-cell transcriptional assessment and functional circuit characterization of neuron types within the mouse entopeduncular nucleus (EP) Overall design: Transcriptional profilingof EP neurons from P60-70 C57BL/6 male mice; three types were identified, characterized, and incorporated into a synaptic-circuit model of basal ganglia please note that Replicate 2 was lost experimentally and not included, so n=3 replicates total
Publication Title
Genetically Distinct Parallel Pathways in the Entopeduncular Nucleus for Limbic and Sensorimotor Output of the Basal Ganglia.
Sample Metadata Fields
Sex, Specimen part, Cell line, 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- Mus musculus
- 174 Downloadable Samples
- NextSeq 500
Description
Single cell RNA sequencing of FACS purified mouse microglia from embryogenesis to old age, and following injury using a demyelinating mouse model. Overall design: 41 total animals, 3-4 replicates per timepoint and condition. E14.5, P4/P5, P30, P100, P540, and Injury
Publication Title
Single-Cell RNA Sequencing of Microglia throughout the Mouse Lifespan and in the Injured Brain Reveals Complex Cell-State Changes.
Sample Metadata Fields
Sex, Cell line, Treatment, Subject
View Samples- Mus musculus
- 38 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302), Affymetrix Mouse Expression 430A Array (moe430a)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 34 Downloadable Samples
Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
Myocardial infarction (MI) often results in left ventricular (LV) remodeling followed by heart failure (HF). It is of great clinical importance to understand the molecular mechanisms that trigger transition from compensated LV injury to HF and to identify relevant diagnostic biomarkers. In this study, we performed transcriptional profiling of LVs in rats with a wide range of experimentally induced infarct sizes and of peripheral blood mononuclear cells (PBMCs) in animals that developed HF.
Publication Title
Transcriptional profiling of left ventricle and peripheral blood mononuclear cells in a rat model of postinfarction heart failure.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 19 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a), Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
3 subtypes of cortical projection neurons were purified by fluorescence-activated cell sorting (FACS) at 4 different stages of development from mouse cortex. A detailed description of the data set is described in Arlotta, P et al (2005) and Molyneaux, BJ et al (2009). The hybridization cocktails used here were originally applied to the Affymetrix mouse 430A arrays and submitted as GEO accession number GSE2039. The same hybridization cocktails were then applied to the Affymetrix mouse 430 2.0 arrays, and those data are contained in this series.
Publication Title
Novel subtype-specific genes identify distinct subpopulations of callosal projection neurons.
Sample Metadata Fields
Specimen part
View Samples- Rattus norvegicus
- 9 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
In hypertension, abnormal regulation of microcirculation and endothelial dysfunction enhances vulnerability to hypertensive brain damage. In addition to lowering blood pressure, blockade of Angiotensin II AT1 receptors protects against stroke and stress in different animal models and this treatment may be of therapeutic advantage. We studied gene expression using Affymetrix Rat Genome U34A arrays from brain microvessels of spontaneously hypertensive rats (SHR) and their normotensive Wistar Kyoto controls (WKY) rats treated with an AT1 antagonist (candesartan, 0.3 mg/kg/day) or vehicle via osmotic minipumps for 4 weeks.
Publication Title
AT1 receptor blockade regulates the local angiotensin II system in cerebral microvessels from spontaneously hypertensive rats.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 14 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
M cells are the main site of bacterial translocation in the intestine. We used the in vitro M cell model to study the effect of the commensal bacteria; Lactobacillus salivarius, Eschericha coli and Bacteroides fragilis, on M cell gene expression.
Publication Title
Differential intestinal M-cell gene expression response to gut commensals.
Sample Metadata Fields
Specimen part, Treatment
View Samples