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SRP095533
Danio rerio
30 Downloadable Samples
IlluminaHiSeq2000
Description
Regeneration requires cells to regulate proliferation and patterning according to their spatial position. Positional memory is a property that enables regenerating cells to recall spatial information from the uninjured tissue. Positional memory is hypothesized to rely on gradients of molecules, few of which have been identified. Here, we quantified the global abundance of transcripts, proteins and metabolites along the proximodistal axis of caudal fins of uninjured and regenerating adult zebrafish. Using this approach, we uncovered complex overlapping expression patterns for hundreds of molecules involved in diverse cellular functions, including developmental and bioelectric signaling as well as amino acid and lipid metabolism. Moreover, 32 genes differentially expressed at the RNA level had concomitant differential expression of the encoded proteins. Thus, the identification of proximodistal differences in levels of RNAs, proteins, and metabolites will facilitate future functional studies of positional memory during appendage regeneration. Overall design: RNA-seq was performed on 5 biological replicates for each of 3 positions along the proximodistal axis of the caudal fin; proximal, middle and distal (15 total samples). Each biological replicate was a pool of fin regions cut from 2 male and 2 female zebrafish.
Publication Title
Transcriptomic, proteomic, and metabolomic landscape of positional memory in the caudal fin of zebrafish.
Sample Metadata Fields
No sample metadata fields
View Samples- Danio rerio
- 1 Downloadable Sample
Description
Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation.
Publication Title
Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
Description
Mammary alveologenesis is abrogated in the absence of the transcription factors STAT5A/5B that mediate cytokine signaling. To reveal the underlying causes for this developmental block we studied mammary stem and progenitor cells. While loss of STAT5A/5B did not affect the stem cell population and their ability to form mammary ducts, luminal progenitors were greatly reduced and unable to form alveoli during pregnancy. Temporally-controlled expression of transgenic STAT5A in mammary epithelium lacking STAT5A/5B restored the luminal progenitor population and rescued alveologenesis in a reversible fashion in vivo. Taken together, STAT5A is necessary and sufficient for the establishment of luminal progenitor cells.
Publication Title
Development of mammary luminal progenitor cells is controlled by the transcription factor STAT5A.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 30 Downloadable Samples
Description
Mndal, a new interferon-inducible family member, is highly polymorphic, suppresses cell growth and may modify plasmacytoma susceptibility.
Publication Title
Mndal, a new interferon-inducible family member, is highly polymorphic, suppresses cell growth, and may modify plasmacytoma susceptibility.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 12 Downloadable Samples
Description
The etiology of autoimmune hepatitis is poorly understood but likely involves Th1 cells producing IFN-. BALB/c background TGF-1-/- mice rapidly develop fulminant Th1-mediated autoimmune hepatitis. Our aims are to profile liver gene expression in TGF-1-/- mice, to identify gene expression pathways dependent on IFN- as possible targets for rational therapy, and to test potential targets directly in vivo in mice.
Publication Title
The role of Ifng in alterations in liver gene expression in a mouse model of fulminant autoimmune hepatitis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 14 Downloadable Samples
Description
To characterized the changes in gene expression during the differentiation of TS cells. TS cells can be derived from two time point during embryogenesis, cell lines tested were from each of these time points.
Publication Title
Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 10 Downloadable Samples
Description
To identify whether Cdx2 or Gata3 can activate trophoblast specific gene expression when expressed in R1 ES cells. To assess the dependency of Gata3 activity on Cdx2, Gata3 was also expressed in Cdx2-null ES cells.
Publication Title
Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 64 Downloadable Samples
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A mouse model of the most aggressive subgroup of human medulloblastoma.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 64 Downloadable Samples
Description
Mouse models of medulloblastoma are compared to human subgroups through microarray expression and other measures
Publication Title
A mouse model of the most aggressive subgroup of human medulloblastoma.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
Description
BMPR2 mutation causes pulmonary arterial hypertension (PAH); ACE2 treatment can resolve established BMPR2-mediated PAH. The purpose of this study was to uncover the molecular mechanism behind this.
Publication Title
Cytoskeletal defects in Bmpr2-associated pulmonary arterial hypertension.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples