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Mus musculus
134 Downloadable Samples
NextSeq 500
Description
Cellular function is strongly dependent on surrounding cells and environmental factors. Current technologies are limited in characterizing the spatial location and unique gene-programs of cells in less structured and dynamic niches. Here we developed a method (NICHE-seq) that combines photoactivatable fluorescent reporters, two-photon microscopy and single-cell RNA-seq to infer the cellular and molecular composition of niches. We applied NICHE-seq to examine the high-order assembly of immune cell networks. NICHE-seq is highly reproducible in spatial tissue reconstruction, enabling identification of rare niche-specific immune subpopulations and unique gene-programs, including natural killer cells within infected B cell follicles and distinct myeloid states in the marginal zone. This study establishes NICHE-seq as a broadly applicable method for elucidating high-order spatial organization of cell types and their molecular pathways. Overall design: Transcriptional profiling of single cells from the specific immune niches in the lymph node and spleen, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500
Publication Title
Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Drosophila melanogaster
- 33 Downloadable Samples
Affymetrix Drosophila Genome 2.0 Array (drosophila2), Affymetrix Drosophila Genome Array (drosgenome1)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component.
Sample Metadata Fields
No sample metadata fields
View Samples
GSE7646- Drosophila melanogaster
- 4 Downloadable Samples
Affymetrix Drosophila Genome Array (drosgenome1)
Description
CLK targets from fly heads using the TIM-GAL4; UAS-CLKGR line
Publication Title
Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component.
Sample Metadata Fields
No sample metadata fields
View Samples GSE7652- Drosophila melanogaster
- 10 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
6 Timepoint microarray from control strain
Publication Title
Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component.
Sample Metadata Fields
No sample metadata fields
View Samples GSE7651- Drosophila melanogaster
- 9 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
6 Timepoints from 5073 strain
Publication Title
Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component.
Sample Metadata Fields
No sample metadata fields
View Samples GSE7644- Drosophila melanogaster
- 4 Downloadable Samples
- Affymetrix Drosophila Genome Array (drosgenome1)
Description
Experiments performed in S2 cells to identify direct CLK targets
Publication Title
Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component.
Sample Metadata Fields
No sample metadata fields
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Affymetrix Drosophila Genome 2.0 Array (drosophila2)
Description
S2 cells transfected with pAc-Clk or empty vector
Publication Title
Clockwork Orange is a transcriptional repressor and a new Drosophila circadian pacemaker component.
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 25 Downloadable Samples
- Affymetrix Rat Gene 1.0 ST Array (ragene10st)
Description
We used microarrays to determine the effect of prenatal nicotine exposure on gene expression profiles in the striatum of adolescent rats. We found a number of immediate early genes to be differentially expressed due to food-restriction.
Publication Title
Long-term effects of gestational nicotine exposure and food-restriction on gene expression in the striatum of adolescent rats.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 24 Downloadable Samples
- IlluminaHiSeq2000
Description
miRNA-1343 is an uncharacterized miRNA predicted to target a number of genes involved in epithelial cell function including TGF-beta signaling, cell adhesion, and cell proliferation. We transiently overexpressed miRNA-1343 or a non-targeting control miRNA in A549 and 16HBE14o- human airway cell lines. As predicted, RNA-seq following miRNA-1343 overexpression showed significant downregulation of genes involved in these pathways. Furthermore, genes involved in cholesterol and lipid biosynthesis were found to be significantly upregulated by miRNA-1343 overexpression. Overall design: mRNA profiles from A549 and 16HBE14o- cells transiently transfected with miRNA-1343 or a negative control (NC) miRNA, in quintuplicate.
Publication Title
miR-1343 attenuates pathways of fibrosis by targeting the TGF-β receptors.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
ARC (NSC 188491, SMA-491), 4-amino-6-hydrazino-7-beta-d-ribofuranosyl-7H-pyrrolo-(2,3-d)-pyrimidine-5-carboxamide, is a nucleoside analog with profound in vitro anti-cancer activity. First identified in a high-throughput screen for inhibitors of p21 mRNA expression, subsequent experiments showed that ARC also repressed expression of hdm2 and survivin, leading to its classification as a global inhibitor of transcription 1. The following Hu U133 plus 2.0 arrays represent single time point (24 hour) gene expression analysis of transcripts altered by ARC treatment. Arrays for the other compounds (sangivamycin and doxorubicin) are included as comparators.
Publication Title
ARC (NSC 188491) has identical activity to Sangivamycin (NSC 65346) including inhibition of both P-TEFb and PKC.
Sample Metadata Fields
No sample metadata fields
View Samples