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Mus musculus
8 Downloadable Samples
Description
Cohesin, which consists of SMC1, SMC3, Rad21 and either SA1 or SA2, topologically embraces the chromatin fibers to hold sister chromatids together and to stabilize chromatin loops. Increasing evidence indicates that these loops are the organizing principle of higher-order chromatin architecture, which in turn is critical for gene expression. To determine how cohesin contributes to the establishment of tissue-specific transcriptional programs, we compared genome-wide cohesin distribution, gene expression and chromatin architecture in cerebral cortex and pancreas from adult mice. More than one third of cohesin binding sites differ between the two tissues and these are enriched at the regulatory regions of tissue-specific genes. Cohesin colocalizes extensively with the CCCTC-binding factor (CTCF). Cohesin/CTCF sites at active enhancers and promoters contain, at least, cohesin-SA1 whereas either cohesin-SA1 or cohesin-SA2 are present at active promoters independently of CTCF. Analyses of chromatin contacts at the Protocadherin gene cluster and the Regenerating islet-derived (Reg) gene cluster, mostly expressed in brain and pancreas respectively, revealed remarkable differences in the architecture of these loci in the two tissues that correlate with the presence of cohesin. Moreover, we found decreased binding of cohesin and reduced transcription of the Reg genes in the pancreas of SA1 heterozygous mice. Given that Reg proteins are involved in the control of inflammation in pancreas, such reduction may contribute to the increased incidence of pancreatic cancer reported in these animals. Overall design: Examination of the relationship between gene expression, genome wide cohesin distribution and chromatin structure
Publication Title
The contribution of cohesin-SA1 to gene expression and chromatin architecture in two murine tissues.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 10 Downloadable Samples
- Illumina HiSeq 2000
Description
Changes in gene expression caused by CREBBP/EP300 bromodomain inhibitors in a CML cell line Overall design: K562 cells were treated with CBP30 and I-CBP112 and changes in gene expression were evaluated by RNA-seq
Publication Title
CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation.
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Sample Metadata Fields
Cell line, Treatment, Subject
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SRP068961- Homo sapiens
- 8 Downloadable Samples
- IlluminaHiSeq2000
Description
Antiprolifereative effects of CREBBP/EP300 inhibitors were tested in human leukemia and lymphoma cell lines and the molecular mechanisms responsible for such effects were explored. Overall design: K562 cells were treated with CBP-30 (CREBBP/EP300 bromodomain inhibitor), C646 (CREBBP/EP300 HAT activity inhibitor) and JQ1 (BRD4 inhibitor) and changes in gene expression were evaluated by RNA-seq.
Publication Title
CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
- Illumina HiSeq 2500
Description
Dermal lymphatics form a network that connects all the hair follicles in skin and localize in proximity to the Hair Follicle Stem Cell. RNA sequencing analyses of isolated dermal lymphatics at two different time points of the hair follicle cycle (P55 and P70) indicate the existence of dynamic signaling networks associated with lymphatic remodeling, immune trafficking, and HF signaling. Overall design: Prox1CreERT2; ROSA26-LSL-eYFP mice of P55 (Mid Telogen) and P70 (Late telogen) were sacrificed and eYFP positive cells were isolated from the backskin.
Publication Title
Lymphatic vessels interact dynamically with the hair follicle stem cell niche during skin regeneration in vivo.
Alternate Accession IDs
Sample Metadata Fields
Treatment, Subject
View Samples- Mus musculus
- 15 Downloadable Samples
- Illumina HiSeq 2000
Description
RNA sequencing of T-ALL tumors derived from genetically modified mouse models: CIC loss-of-function, HRASG12V driven from the Kras promoter and Trp53 KO. Results provide insight into the role of the RAS/CIC axis in T-ALL development. Overall design: RNA-Sequencing of 5 CIC LOF, 3 K:HrasG12V and 4 Trp53 KO T-ALL murine tumor samples.
Publication Title
Inactivation of Capicua in adult mice causes T-cell lymphoblastic lymphoma.
Alternate Accession IDs
Sample Metadata Fields
Cell line, Treatment, Subject
View Samples- Mus musculus
- 5 Downloadable Samples
- Illumina HiSeq 2000
Description
CXCL5, a strong neutrophil-chemoattractant, has been reportet to be expressed in different cancer entities with diverse outcomes in disease progression. Contradictory outcome in disease progression in different tumor entities might be explained by a tumor type specific expression pattern of chemokines, chemokine receptors and growth factors that act in concert with CXCL5. This study evaluates the impact of CXCL5 expression on the tumor mircoenvironment in a syngeneic mouse melanoma model. Overall design: 105 B16F1 and B16F1-CXCL5 murine melanoma were injected intradermally into the flank skin of C57BL/6 J mice. Primary tumors were grown up to 250-350mm³, excised, snap frozen and then processed for RNA sequencing.
Publication Title
CXCL5 as Regulator of Neutrophil Function in Cutaneous Melanoma.
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Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Homo sapiens
- 22 Downloadable Samples
- IlluminaHiSeq2000
Description
The histone methyltransferase NSD2/WHSC1/MMSET is overexpressed in a number of solid tumors but its contribution to the biology of these tumors is not well understood. Here, we describe that NSD2 contributes to the proliferation of a subset of lung cancer cell lines by supporting oncogenic RAS transcriptional responses. Co-treatment with MEK and BRD4 inhibitors causes co-operative inhibitory responses on cell growth. While these inhibitors converge in the downregulation of genes associated with cancer-acquired super-enhancers, NSD2 inhibition complements their action by affecting the expression of clusters of genes embedded in megabase-scale regions marked with H3K36me2. Thus, combinatorial therapies using MEK or BRD4 inhibitors together with NSD2 inhibition ensure a more comprehensive inhibition of oncogenic RAS-driven transcription programs. Overall design: H1299 cells were transduced with doxycycline (dox) inducible shRNAs (sh3 or sh5) againts NSD2 and with non target shRNA (shNT). Changes in gene expression (RNA-seq) and H3K36me2 (ChIP-seq) caused by depletion of NSD2 and indicated treatments were assessed. Two replicates (Rep) for RNA-seq and three replicates for ChIP-seq were included.
Publication Title
NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 16 Downloadable Samples
- Illumina HiSeq 2000, Illumina Genome Analyzer IIx
Description
c-Fos, a member of the stress-activated Activator Protein 1 (AP-1) transcription factor family, is expressed in human hepatocellular cancer (HCC). Using genetically engineered mouse models (GEMMs) we show that hepatocyte-specific expression of c-Fos leads to a proliferative, de-differentiated phenotype, whereas hepatocyte-specific deletion of c-Fos protects against diethylnitrosamine (DEN)-induced liver cancer. Furthermore, c-Fos-expressing livers resemble human HCCs based on expression profiles. In the present RNA seq, we intend to analyze the transcriptomic profile of livers at 2 and 4 mo hepatocyte-specific c-Fos expression compared to the corresponding age-matched control mice. Moreover, we analyzed livers of mice with hepatocyte-specific deletion c-Fos at 48h after DEN treatment compared to identically treated control mice. Overall design: The general idea was to analyze the transcriptomic profile of hepatocyte-specific c-Fos over-expressing livers at 2 and 4 mo expression. Hereby, a hepatocyte-specific doxycycline (Dox)-switchable mouse model was (LAP-tTA; col1a1:Tet-O-fosFlag) was generated and c-Fos expression was induced at the age of 3 weeks by removal of doxycycline. Each sample LaptTA-fos-MUT represents an individual hepatocyte-specific c-fos expressing mouse at the indicated time-point and the corresponding identically treated control mouse LaptTA-fos-CO. Moreover, the transcriptomic profile of livers with hepatocyte-specific deletion of c-Fos at 48h after diethylnitrosamine (DEN)-induced liver cancer initiation was analyzed. For hepatocyte-specific knock-out of c-Fos, mice with conditional alleles of c-fos and the Alfp-Cre transgene were used. Control mice only carried the Alfp-Cre transgene. At the age of 8 weeks these mice were injected with 100mg/kg DEN. Each sample AlfpCre-fos-MUT_DEN represents an individual hepatocyte-specific c-fos knock-out mouse 48h after DEN and the identically treated control mouse AlfpCre-fos-CO-Cre+_DEN.
Publication Title
Liver carcinogenesis by FOS-dependent inflammation and cholesterol dysregulation.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples- Mus musculus
- 7 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
NANOG is a key pluripotency factor in embryonic stem cells that is frequently expressed in squamous cell carcinomas (SCCs). However, a direct link between NANOG and SCCs remains to be established. Here, we show that inducible overexpression of NANOG in mouse skin epithelia dramatically promotes the formation of carcinomas upon chemical carcinogenesis. Gene expression analyses in pre-malignant skin indicate that NANOG induces a large set of genes associated to stemness and to epithelial-mesenchymal transition (EMT). Overall design: 4 papillomas from different control mice (CTR), and 3 papillomas from different transgenic Nanog overexpressing mice (TG)
Publication Title
The pluripotency factor NANOG promotes the formation of squamous cell carcinomas.
Alternate Accession IDs
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 21 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
RNA-seq was performed using the RNA extracted from the bottom half of right lobe of mouse livers. Mice fall into two groups, mutant group which express ectopic hURI and their control littermates which do not express hURI. Two time points were considered in the study, 1-week-old mice, expressing hURI since 1 week (n =3, 4 for control and mutant, respectively) and 8-week-old mice expressing hURI since 8 week (n= 4, 3 for control and mutant, respectively), as hURI is expressed since conception. Overall design: Determination of differentially expressed transcripts over two time points (1 week and 8 weeks) in mouse livers expressing hURI (1 week and 8 weeks).
Publication Title
Inhibition of de novo NAD(+) synthesis by oncogenic URI causes liver tumorigenesis through DNA damage.
Alternate Accession IDs
Sample Metadata Fields
Specimen part, Subject
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