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Mus musculus
37 Downloadable Samples
Illumina HiSeq 2000
Description
Purpose: Due to its high metastatic proclivity, pancreatic ductal adenocarcinoma (PDAC) is one of the most deadly types of cancer. Therefore, it is imperative to better understand how the disease spreads as it progresses. Using a novel genetically engineered mouse model that allows us to isolate a subpopulation of cancer cells with superior metastatic capacity, we show that this aggressive phenotype correlates exclusively with a strong hypoxia signature. We subsequently identified the novel hypoxia-inducible gene Blimp1, which appears to play a critical role in regulating the hypoxic response upon its induction. Furthermore, genetic ablation of Blimp1 greatly reduces the level of metastasis in a PDAC mouse model. The nature of this Blimp1-regulated hypoxia signature is very unstable, since the seeded metastatic lesions mostly re-adopt similar transcriptomic profiles as the primary tumors. In conclusion, our results offer a potential mechanistic insight into how hypoxia drives metastasis in PDAC. Methods: Pure, paired GFP-negative/Tomato-positive and GFP-positive/Tomato-positive cancer cells or pure Tomato-positive cancer cells were sorted from primary PDAC samples from 6 KPC-colors mice or KPCT mice, respectively, with the following criteria: single cell based on FSC-A/H; CD45-negative; CD31-negative; Ter119-negative; F4/80-negative; DAPI-negative; and Tomato-positive. RNA were extracted from 10^4 to 5x10^4 freshly sorted cancer cells using AllPrep DNA/RNA Micro Kit (Qiagen). RNA quality was assessed with the RNA6000 PicoAssay kit by using the Bioanalyzer 2100 (Agilent). All ex vivo RNA samples used for RNA-seq analyses had an RIN > 8.0. Total RNA (15 ng/sample) was used for cDNA synthesis and amplification with the Ovation RNA-Seq system (NuGEN Technologies, Inc.). Subsequently, the amplified DNA samples were fragmented through sonication (Covaris model S1) and subjected to library preparation using the Illumina TruSeqTM DNA sample preparation kit (Low-Throughput protocol) according to manufacturer''s protocol. The quality of purified cDNA library products was confirmed by bioanalyzer and prepared for cluster generation on HiSeq paired-end flow cells using the CBot automated cluster generation system followed by sequencing on HiSeq 2000 machines. We obtained 101bp, paired-end reads from fragments of an average length of 250bp. Subsequently, RNA-Seq reads were aligned to the mouse genome (mm10) using the STAR aligner with standard input parameters (Dobin et al., 2013). The number of reads uniquely aligned to exons of individual genes were counted with HTSeq against the UCSC KnownGene (mm10) transcriptome (Anders et al., 2015). Results: Compared to the GFP-negative counterparts, GFP-positive pure PDAC cancer cells express higher levels of genes that are highly enriched with hypoxia signature. Additionally, compared to the GFP-negative counterparts, GFP-positive pure PDAC cancer cells express lower levels of cell cycle-related genes. In contrast, pure cancer cells isolated based on locations reveal few consistent differentially expressed genes between primary tumor and liver metastases; no consistent differentially expressed gene between primary tumor and lymph node metastases. Conclusions: Transcriptome profiles of both GFP-negative/positive PDAC cancer cells suggest that Hmga2/GFP-expressing cancer cells are highly enriched for signatures that correspond to cells residing within hypoxic enrivonment. Overall design: Freshly sorted GFP/Hmga2-positive and GFP/Hmga2-negative PDAC cancer cells derived from tumors of 6 KPCT;Hmga2-CK/+ (KPC-colors) mice were subjected to transcriptome profiling by paired-end RNA-Seq (total of 6 pairs of samples with overall 12 samples). Additionally, pure Tomato-positive PDAC cancer cells isolated from different anatomical locations were also subjected to transcriptome profiling by paired-end RNA-Seq (n = 23, not including technical replicates).
Publication Title
BLIMP1 Induces Transient Metastatic Heterogeneity in Pancreatic Cancer.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 14 Downloadable Samples
- Illumina Genome Analyzer II
Description
No description.
Publication Title
Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
MicroRNAs inhibit gene expression by recruiting the RNA-induced silencing complex (RISC) to mRNAs in a process termed RNA interference (RNAi). While it is generally accepted that RNAi modulates gene expression pervasively, the number of mRNAs bound and repressed by miRNAs in vivo in individual cell types remains unknown, with estimates ranging from a few hundred genes to many thousands. We examined microRNA activities in primary cells by combining genetic loss of function with RNA-sequencing, quantitative proteomics and High-Throughput Sequencing of RNA isolated by Crosslinking Immunoprecipitation (HITS-CLIP), focusing on miR-144/451, the most highly expressed microRNA locus during red blood cell (RBC) formation. We show that Argonaute (Ago) protein binds over one thousand different mRNAs in a miR-144/451-dependent manner, accounting for one third of all Ago-bound mRNAs. However, only about 100 mRNAs are stabilized in RBC precursors after ablation of the miR-144/451 locus. Thus, Ago-miRNA complexes destabilize only a small subset of bound mRNAs, probably no more than a few hundred in erythroblasts under physiological conditions. Our integrated approach identified more than 50 new miR-144/451 target mRNAs, including Cox10, which facilitates assembly of the mitochondrial cytochrome c oxidase (COX) electron transport complex. Loss of miR-144/451 resulted in increased Cox10 expression, accumulation of the COX complex, and increased mitochondrial membrane potential with no change in mitochondrial mass. Thus, miR-144/451 represses mitochondrial respiration during erythropoiesis by inhibiting Cox10. Overall design: HITS-CLIP analysis of 3 WT mice fetal livers vs 3 miR-144/451 KO mice fetal livers
Publication Title
Regulation of gene expression by miR-144/451 during mouse erythropoiesis.
Sample Metadata Fields
Cell line, Subject
View Samples- Drosophila melanogaster
- 5 Downloadable Samples
Affymetrix Drosophila Genome Array (drosgenome1)
Description
5 day RNAi treatment to knockdown Enigma, CG9006, a Drosophila mitochondrial protein with homology to acyl-CoA dehydrogenases.
Publication Title
Enigma, a mitochondrial protein affecting lifespan and oxidative stress response in Drosophila.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Muscle stem cells (MuSC) change molecular and functional properties during development. Using a transgenic Tg:Pax7-nGFP mice, we FACS-isolated MuSC from embryonic (E12.5) and foetal (E17.5) stages to understand the differences and similarities amongst the myogenic stem/progenitor populations.
Publication Title
Cell-autonomous Notch activity maintains the temporal specification potential of skeletal muscle stem cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 14 Downloadable Samples
- Affymetrix Mouse Gene 2.0 ST Array (mogene20st)
Description
Mouse neural stem cells were generated from conditional knockout mice (Cicflox/flox) or the wild trype control mice (Cic+/+). Cic is conditionally knocked out following expression of Cre-recombinase. Cre-recombinase was incorporated in vitro via adenoviral-Cre transduction.
Publication Title
<i>Cic</i> Loss Promotes Gliomagenesis via Aberrant Neural Stem Cell Proliferation and Differentiation.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 9 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
ATC are among the most lethal malignancies, for which there is no effective treatment.
Publication Title
Cell cycle deregulation and TP53 and RAS mutations are major events in poorly differentiated and undifferentiated thyroid carcinomas.
Sample Metadata Fields
Sex, Specimen part
View Samples
GSE98424- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Mouse Hammer toe (Hm) shows syndactyly. To reveal the molecular mechanisms of Hm phenotype, we performed microarray analysis to search differencially expressed genes in Hm limb.
Publication Title
Enhancer adoption caused by genomic insertion elicits interdigital <i>Shh</i> expression and syndactyly in mouse.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Gene 2.1 ST Array (mogene21st)
Description
To define and compare the genome-wide transcriptional signatures of Notch1+ cells in intestinal tumors and in normal ISCs we performed Affymetrix analyses of these two populations.
Publication Title
Lineage tracing of Notch1-expressing cells in intestinal tumours reveals a distinct population of cancer stem cells.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
A nxnl2 knockout mouse model was created and the transcriptome used to demonstrate that the retina is compromised by the absence of nxnl2.
Publication Title
Nxnl2 splicing results in dual functions in neuronal cell survival and maintenance of cell integrity.
Sample Metadata Fields
Specimen part
View Samples