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SRP067494
Mus musculus
22 Downloadable Samples
NextSeq 500
Description
Analysis of gene expression by astrocytes or non-astrocyte cells in spinal cord injury (SCI) lesions may lead to the identification of molecules that impact on axon regrowth. We conducted genome-wide RNA sequencing of (i) immunoprecipitated astrocyte-specific ribosome-associated RNA (ramRNA) from WT or STAT3-CKO astrocytes, and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells in the same tissue samples 14 days following SCI. DOI: 10.1038/nature17623 Overall design: Young adult female mGFAP-Cre-RiboTag or mGFAP-Cre-RiboTag-STAT3-LoxP mice underwent severe crush SCI at thoracic level 10. 14 days following SCI, the central 3mm of the SCI lesion was extracted, homogenized and (i) astrocyte-specific ribosome-associated RNA (ramRNA) precipitated via a hemagglutinin (HA) tag targeted to either WT (n=4) or STAT3-CKO (n=3) astrocytes, and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells in the same tissue samples. Sex and age-matched mGFAP-Cre-RiboTag mice served as uninjured controls (n=4).
Publication Title
Astrocyte scar formation aids central nervous system axon regeneration.
Sample Metadata Fields
Specimen part, Subject
View Samples- Rattus norvegicus
- 167 Downloadable Samples
Affymetrix Rat Genome 230 2.0 Array (rat2302)
Description
We used microarray gene expression analyses to unveil the mechanisms underlying NT-3-chitosan-induced spinal cord regeneration.
Publication Title
Transcriptome analyses reveal molecular mechanisms underlying functional recovery after spinal cord injury.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 23 Downloadable Samples
- NextSeq 500
Description
Comparison of genomic data from astrocytes and non-astrocyte cells from mice with or without FGF+EGF after SCI. We conducted genome-wide RNA sequencing of (i) immunoprecipitated astrocyte-specific ribosome-associated RNA (ramRNA) and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells, from spinal cord tissue of mice recieving i) SCI alone, ii) SCI+hydrogel depot containing FGF+EGF, or iii) SCI+empty hydrogel depot. Overall design: Young adult mGFAP-Cre-RiboTag mice underwent severe crush SCI at thoracic level 10. Hydrogel depots were injected two days post-injury. At 14 days following SCI, the central 3mm of the SCI lesion was extracted, homogenized and (i) astrocyte-specific ribosome-associated RNA (ramRNA) precipitated via a hemagglutinin (HA) tag targeted to astrocytes, and (ii) the non-precipitated (flow-through) RNA deriving from non-astrocyte cells in the same tissue samples.
Publication Title
Required growth facilitators propel axon regeneration across complete spinal cord injury.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 29 Downloadable Samples
- Illumina HiSeq 2500
Description
Skeletal muscle insulin resistance, decreased phosphatidylinositol 3-kinase (PI3K) activation and altered mitochondrial function are hallmarks of type 2 diabetes. We created mice with a muscle-specific knockout of p110a or p110ß, the two major catalytic subunits of PI3K. We find that mice with muscle-specific knockout of p110a, but not p110ß, display impaired muscle insulin signaling and reduced muscle size due to enhanced proteasomal and autophagic activity. Despite insulin resistance and muscle atrophy, M-p110aKO mice show decreased serum myostatin, increased mitochondrial mass, increased mitochondrial fusion visualized by intravital microscopy, and increased PGC1a expression, especially PCG1a2 and PCG1a3. This leads to enhanced mitochondrial oxidative capacity, striking increases in muscle NADH content, and higher muscle free radical release measured in vivo using pMitoTimer reporter. Thus, p110a is the dominant catalytic isoform of PI3K in muscle in control of insulin sensitivity and muscle mass, and has a unique role in mitochondrial homeostasis in skeletal muscle. Overall design: All studies were performed in male mice on C57BL/6J background. Muscle-specific p110alpha or p11beta knockout mice were generated by crossing mice carrying the Cre recombinase gene driven by the human alpha-skeletal actin (HSA) promoter (Jackson Laboratories Stock Number: 006149) with mice carrying either floxed p110alpha or p110beta alleles in which exon 1 of p110alpha or exon 2 of p110bet was flanked with loxP sites. Skeletal muscle from 2-3-month-old male mice was harvested and RNA was extracted using Trizol. Gene expression profiling was performed using NEBNext mRNA Sample Prep Master Mix kit (NEB) by BioPolymers Facility at Harvard Medical School. Reads were aligned to the mouse genome (GRCm38) using STAR aligner and counted with Subread featureCounts.
Publication Title
Role of p110a subunit of PI3-kinase in skeletal muscle mitochondrial homeostasis and metabolism.
Sample Metadata Fields
Sex, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 59 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
A gene expression profiling study was conducted in which skin biopsy samples were collected for RNA extraction and hybridization to microarrays from patients with moderate-to-severe psoriasis who participated in the phase 1, guselkumab first-in-human randomized, double-blind, placebo-controlled trial.
Publication Title
Guselkumab (an IL-23-specific mAb) demonstrates clinical and molecular response in patients with moderate-to-severe psoriasis.
Sample Metadata Fields
Subject
View Samples