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SRP066440
Mus musculus
383 Downloadable Samples
NextSeq 500
Description
Two 96-well plates per genotype wild type and Myd88 knockout, 4 hour time series in 0.5 hr increments Overall design: Myd88 BMDM transcriptional profiling to complement TF-seq data
Publication Title
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject, Time
View Samples- Mus musculus
- 120 Downloadable Samples
- NextSeq 500
Description
Bone marrow derived macrophages treated with small molecules and stimulated with LPS Overall design: Wild-type BMDMs pretreated with small molecules for 30 minutes prior to stimulation with LPS
Publication Title
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject, Time
View Samples- Mus musculus
- 96 Downloadable Samples
- NextSeq 500
Description
Bone marrow derived macrophages treated with small molecules and stimulated with LPS Overall design: Wild-type BMDMs pretreated with small molecules for 30 minutes prior to stimulation with LPS
Publication Title
Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.
Sample Metadata Fields
Sex, Age, Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 13 Downloadable Samples
Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Therapeutic hypothermia is a clinically effective treatment for various hypoxic and ischemic conditions, but the associated molecular mechanisms remain unclear. To gain insight into hypothermia-induced transcriptional response, mouse embryonic fibroblasts were exposed to mild hypothermia (32C) or normothermia (37C) for increasing time periods. We aimed to identify genes with temporally near-monotonic response as the most obvious candidates for mediating the therapeutic effects of hypothermia.
Publication Title
Estimating differential expression from multiple indicators.
Sample Metadata Fields
Specimen part, Time
View Samples- Mus musculus
- 224 Downloadable Samples
- Illumina HiSeq 2000
Description
Transcriptional profiling of murine dendritic cells stimulated with LPS and IFNg after shRNA knockdown of redox regulators. Overall design: shRNA targeting redox regulators were delivered to bone marrow derived dendritic cells. Cells were stimulated with LPS and IFNg prior to transcriptional profiling by RNAseq over a time course. Each sample sequenced on two Illumina lanes.
Publication Title
Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Drosophila melanogaster
- 72 Downloadable Samples
- Illumina HiSeq 2000
Description
Genome control is operated by transcription factors (TF) controlling their target genes by binding to promoters and enhancers. Conceptually, the interactions between TFs, their binding sites, and their functional targets are represented by gene regulatory networks (GRN). Deciphering in vivo GRNs underlying organ development in an unbiased genome-wide setting involves identifying both functional TF-gene interactions and physical TF-DNA interactions. To reverse-engineer the GRN of eye development in Drosophila, we performed RNA-seq across 72 genetic perturbations and sorted cell types, and inferred a co-expression network. Next, we derived direct TF-DNA interactions using computational motif inference, ultimately connecting 241 TFs to 5632 direct target genes through 24926 enhancers. Using this network we found network motifs, cis-regulatory codes, and new regulators of eye development. We validate the predicted target regions of Grainyhead by ChIP-seq and identify this factor as a general co-factor in the eye network, being bound to thousands of nucleosome-free regions. Overall design: RNA-seq gene expression profiling across Drosophila 3rd instar larval wild type tissues (brain, eye-antennal and wing discs), specific cell types from the eye-antennal disc, sorted by FACS, and genetic perturbations (TF mutants, TF over-expression, and TF RNAi knockdown).
Publication Title
Mapping gene regulatory networks in Drosophila eye development by large-scale transcriptome perturbations and motif inference.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 2000
Description
High throughput massively parallel sequencing on mRNA libraries generated from cortices of bexarotene or vehicle treated APP/PS1 Overall design: Read counts analyzed for differential gene expression using edgeR
Publication Title
RNA-sequencing reveals transcriptional up-regulation of Trem2 in response to bexarotene treatment.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 58 Downloadable Samples
- Illumina HiSeq 2500
Description
We examined the impact of Abca1 deficiency and APOE isoform expression on the response to TBI using 3-months-old, human APOE3+/+ (E3/Abca1+/+) and APOE4+/+ (E4/Abca1+/+) targeted replacement mice, and APOE3+/+ and APOE4+/+ mice with only one functional copy of the Abca1 gene (E3/Abca1+/-; E4/Abca1+/-). TBI-treated mice received a craniotomy followed by a controlled cortical impact (CCI) brain injury in the left hemisphere; sham-treated mice received the same surgical procedure without the impact. We performed RNA-seq using samples from cortices and hippocampi collected at 14 days post-injury, followed by genome-wide differential gene expression analysis. Overall design: We used 3-months-old, human APOE3+/+ (E3/Abca1+/+) and APOE4+/+ (E4/Abca1+/+) targeted replacement mice, and APOE3+/+ and APOE4+/+ mice with only one functional copy of the Abca1 gene (E3/Abca1+/-; E4/Abca1+/-). Groups consisted of 6-8 animals of both genders. TBI-treated mice received a craniotomy followed by a controlled cortical impact (CCI) brain injury in the left hemisphere; sham-treated mice received the same surgical procedure without the impact. We performed RNA-seq using samples from cortices and hippocampi collected at 14 days post-injury from 58 samples, followed by genome-wide differential gene expression analysis.
Publication Title
ABCA1 haplodeficiency affects the brain transcriptome following traumatic brain injury in mice expressing human APOE isoforms.
Sample Metadata Fields
Sex, Treatment, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Ion Torrent Proton
Description
This study shows that the TLR4/MyD88 pathway in intestinal mesenchymal cells promotes intestinal carcinogenesis in the APCmin mouse model. Overall design: 3' RNA-Seq (QuantSeq) profiling of ColVIcre+ wt and MyD88 knockout primary mouse intestinal mesenchymal cells before and after treatment with LPS for 6 hours. 3 replicates per group.
Publication Title
Innate Sensing through Mesenchymal TLR4/MyD88 Signals Promotes Spontaneous Intestinal Tumorigenesis.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Triticum aestivum
- 35 Downloadable Samples
- Affymetrix Wheat Genome Array (wheat)
Description
The wheat gene Lr34 confers partial resistance to all races of Puccinia triticina, the causal agent of wheat leaf rust. However, the biological basis for the exceptional durability of Lr34 is unclear. The Affymetrix wheat genome array was used to identify wheat genes differentially expressed in a compatible interaction (Tc), an R-gene mediated incompatible interaction (Tc-Lr1), and a race non-specific resistance interaction (Tc-Lr34) in response to infection challenge by P. triticina race 1 at anthesis. Transcriptome interrogation was conducted by comparing mock- and P. triticina-inoculated leaves harvested at 3 and 7 days post inoculation (dpi).
Publication Title
Lr34-mediated leaf rust resistance in wheat: transcript profiling reveals a high energetic demand supported by transient recruitment of multiple metabolic pathways.
Sample Metadata Fields
No sample metadata fields
View Samples