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SRP066166
Drosophila melanogaster
176 Downloadable Samples
Illumina HiSeq 2500
Description
We report the application of low cell number sequencing of identifiable Drosophila melanogaster neurons following behavior. We demonstate the feasibility of identifying the transcriptome of 5 Mushroom Body output Neurons and 2 classes of Kenyon Cells. We find these neurons display a diverse repertoire of receptors and signaling transcripts. This information alone seems to be enough to identify each class of neurons in the study. In additional we show that aversive long-term memory induces changes in gene transcript levels in a subset of these neurons. This study provides a framework for identifying neuronal classes in Drosophila melanogaster and gaining insight into the interplay between behavior and gene regulation. Overall design: 5 Mushroom Body output neurons and 2 classes of kenyon cells are used to look at general gene expression and changes following aversive long term memory. Paired control and trained animals were used and a minimum of 4 pairs up to 6 pairs. Animals were of the same background (w1118). Animals were aged and parental matched. Cells were harvested at the same chronological time for the animals across all experiments. All animals were exposed to 1 minute of each odor and 1 minute of a series of 12 5second 60V shocks. This was considered one block and then the animals had spaced training of each block so there was a 10 minute break between 8 blocks of training. Trained animals had an odor paired with a shock, control animals received the shock then the odor stimulus. All cells were harvested usign a patch pipet from living animals on an electrophysiology rig within a half hour of the end of training. Cells were amplified using the Clontech SMARTer Ultra Low Input RNA version 2 High Volume kit. 2 Brain samples were also collected and 3-4 whole fly samples for each genotype were collected to account for background differences across flies.
Publication Title
Cell-Type-Specific Transcriptome Analysis in the Drosophila Mushroom Body Reveals Memory-Related Changes in Gene Expression.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 4 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Bcl11a is a transcription factor known to regulate lymphoid and erythroid development. Recent bioinformatic analysis of global gene expression patterns has suggested a role for Bcl11a in the development of dendritic cell (DC) lineages. We tested this hypothesis by analyzing the development of DC and other lineages in Bcl11a(-/-) mice. We show that Bcl11a is required for expression of IL-7 receptor (IL-7R) and Flt3 in early hematopoietic progenitor cells. The loss of IL-7R(+) common lymphoid progenitors accounts for previously described lymphoid defects in Bcl11a(-/-) mice. In addition, we found severely decreased numbers of plasmacytoid dendritic cells (pDCs) in Bcl11a(-/-) fetal livers and in the bone marrow of Bcl11a(-/-) fetal liver chimeras. Moreover, Bcl11a(-/-) cells show severely impaired in vitro development of Flt3L-derived pDCs and classical DCs (cDCs). In contrast, we found normal in vitro development of DCs from Bcl11a(-/-) fetal liver cells treated with GM-CSF. These results suggest that the persistent cDC development observed in Bcl11a(-/-) fetal liver chimeras reflects derivation from a Bcl11a- and Flt3-independent pathway in vivo.
Publication Title
Bcl11a controls Flt3 expression in early hematopoietic progenitors and is required for pDC development in vivo.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 35 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The present study reveals LMYC and MXD1 as novel regulators of a transcriptional program that is modulated during the maturation of Batf3-dependent dendritic cells (also known as type I classical dendritic cells or cDC1s).
Publication Title
The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
Illumina HumanHT-12 V4.0 expression beadchip, Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
<i>APOL1</i> Renal-Risk Variants Induce Mitochondrial Dysfunction.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Transcriptome Array 2.0 (hta20), Illumina HumanHT-12 V4.0 expression beadchip
Description
To assess differential gene expression by APOL1 renal-risk (2 risk alleles) vs. non-risk (G0G0) genotypes in primary proximal tubule cells (PTCs), global gene expression (mRNA) levels were examined on Affymetrix HTA 2.0 arrays in primary PTCs cultured from non-diseased kidney in African Americans without CKD who underwent nephrectomy for localized renal cell carcinoma.
Publication Title
<i>APOL1</i> Renal-Risk Variants Induce Mitochondrial Dysfunction.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 1 Downloadable Sample
- Affymetrix Human Transcriptome Array 2.0 (hta20), Illumina HumanHT-12 V4.0 expression beadchip
Description
To elucidate pathways whereby apolipoprotein L1 gene (APOL1) G1 and G2 variants facilitate kidney disease in African Americans, human embryonic kidney cells (HEK293) were used to establish doxycycline-inducible (Tet-on) cell lines stably expressing reference APOL1 G0 and its G1 and G2 renal-risk variants. Illumina human HT-12-v4 arrays and Affymetrix HTA 2.0 arrays were employed to generate global gene expression data with doxycycline induction. Significantly altered pathways identified through bioinformatics involved mitochondrial function; results were validated using immunoblotting, immunofluorescence and functional assays.
Publication Title
<i>APOL1</i> Renal-Risk Variants Induce Mitochondrial Dysfunction.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
ES cells differentiated in the presence of the Wnt inhibitor DKK1 fail to express the transcription factor Snail and undergo EMT or mesoderm differentiation. We generated an ES cell line, A2.snail, that induced Snail expression upon addition of doxycycline addition.
Publication Title
Snail promotes the cell-autonomous generation of Flk1(+) endothelial cells through the repression of the microRNA-200 family.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 22 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Dual actions of Meis1 inhibit erythroid progenitor development and sustain general hematopoietic cell proliferation.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Mus musculus
- 10 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The homeodomain protein Meis1 is essential for definitive hematopoiesis and vascular patterning in the mouse embryo. Meis2, another member of the same family, shares 82% protein identities with Meis1. Our present study suggested Meis2 exerts two distinguishable effects in differentiating ES cells. First, it increases the numbers of hematopoietic progenitors and extends their persistence in culture. Second, Meis2 skews hematopoietic differentiation by suppressing erythroid while enhancing megakaryocytic progenitor differentiation. To identify the underlying transcriptional bases of these actions, we carried out microarray analysis to compare the various populations of cells developing in ES differentiation cultures in the presence and absence of Meis2 induction.
Publication Title
Dual actions of Meis1 inhibit erythroid progenitor development and sustain general hematopoietic cell proliferation.
Sample Metadata Fields
Specimen part, Treatment
View Samples