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SRP063060
Mus musculus
12 Downloadable Samples
Illumina HiSeq 2000
Description
Purpose: To identify the impact of 2''-FL supplementation on adaptive response following extensive intestinal resection. Methods: Transcriptomic profiles were obtained from mice undergoing ileocecal recection (8-10 week old male mice) and again at 8 weeks post-surgery. At the time of resection and again at 8 weeks post-op, small bowel samples were obtained from treatment and control animals and submitted for mRNA profiling. During these 8 weeks treatment animals (n=3) received 2''-FL supplementationion while controls (n=3) received only standard diet. Results: We observe enrichment in genes and pathways related to anti-microbial peptides, metabolism, and energy processing. Supplementation of 2''-FL increases energy availability and enhances the adaptive response. Overall design: Male C57BL/6 mice at 8 to 10 weeks of age were submitted to ileocecal recection. Following resection, half were supplemented with 2''-FL for 8 weeks; small bowels were obtained and submitted for mRNA profiling,
Publication Title
The human milk oligosaccharide 2'-fucosyllactose augments the adaptive response to extensive intestinal.
Sample Metadata Fields
Sex, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 29 Downloadable Samples
- Illumina HiSeq 2500
Description
We analyzed gene expression profiles of self-organizing, multi-cellular, 3D liver organoids derived by co-culture of induced Pluripotent Stem Cell and stromal progenitors. We report the RNA-seq results of liver organoid at day0, day2, day4, day6 of co-culture. We also report RNA-seq results of constituent of the liver organoid, which are human iPSC at hepatic specification stage, human Mesenchymal stem cells derived from bone marrow, human umbilical vein endothelial cell. As controls, we also report RNS-seq results of un-differentiated human iPSC, human iPSC at definitive endoderm stage, human liver tissue, and primary cultured human hepatocytes isolated from unused donor livers. Overall design: mRNA profiles of liver organoids and their constituents were generated by deep sequencing, in triplicate, using Illumina HiSeq 2500.
Publication Title
Paracrine signals regulate human liver organoid maturation from induced pluripotent stem cells.
Sample Metadata Fields
Subject, Time
View Samples- Mus musculus
- 13 Downloadable Samples
- Illumina HiSeq 2500
Description
Purpose: Characterize functional alterations in stem cells and paneth cells obtained from young and aged mice, focusing on age-based impairment of intestinal regeneration due to a decline in canonical Wnt signaling. Methods: mRNA profiles of young and aged stem and paneth cells were generated in triplicate (with one additional young paneth sample) using the Illumina HiSeq 2500. Reads that passed quality filters were aligned to the mm10 mouse genome with annotations provided by UCSC. Results: Approximately 10 millions reads were aligned per sample, corresponding to 36186 transcripts -- of these, 19574 exhibited reasonable expression. The effect of age was tested wtihin paneth and stem cells, using unpaired t-tests with a p-value cutoff of 0.05 and fold change cutoff of 1.5. Within paneth cells, 1025 genes were significant; within stem cells, 750 genes exhibited differential regulation. Among the downregulated genes in paneth and stem cells, we observed significant enrichment of canonical Wnt signaling genes. Conclusion: Age-related downregulation of canonical Wnt signaling is involved in the impairment of intestinal regulation upon aging. Overall design: mRNA profiles of paneth and stem cells obtained from proximal intestinal crypts from aged and young male Lgr5 mice were generated using RNAsequencing in triplicate, using Illumina HiSeq 2500.
Publication Title
Canonical Wnt Signaling Ameliorates Aging of Intestinal Stem Cells.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 67 Downloadable Samples
Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The genomic landscape of hepatic tissue affected by nonalcoholic steatohepatitis (NASH) in severely obese adolescents undergoing bariatric surgery is unknown. Our purpose here was to uncover genomic profiles of obese controls, and obese cases with nonalcoholic fatty liver disease (NAFLD), borderline nonalcoholic steatohepatitis, and definite nonalcoholic steatohepatitis, in order to clarify molecular functions, biological processes, and pathways that are dysregulated in nonalcoholic steatohepatitis in the severely obese adolescent.
Publication Title
High Prevalence of Nonalcoholic Fatty Liver Disease in Adolescents Undergoing Bariatric Surgery.
Sample Metadata Fields
Sex, Disease
View Samples- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 1000
Description
Background & Aims: Spasmolytic polypeptide/TFF2-expressing metaplasia (SPEM) is known to emerge following parietal cell loss and during Helicobacter pylori infection, however its role in gastric ulcer repair is unknown. Therefore, we sought to investigate if SPEM plays a role in epithelial regeneration. Methods: Acetic acid ulcers were induced in young (2-3 months) C57BL/6 mice to determine the quality of ulcer repair. Gastric tissue was collected and analyzed to determine the expression of SPEM within the regenerating epithelium. As a comparison to native tissue the expression of SPEM was also identified within cultured gastric mouse-derived organoids. Results: Wound healing in the mice coincided with the emergence of SPEM expressing CD44v within the ulcerated region. The emergence of SPEM was also observed in cultured gastric organoids. Conclusions: These data demonstrate the SPEM may play a role in epithelial regeneration. Conclusions: These data demonstrate the SPEM may play a role in epithelial regeneration. Overall design: 4 samples were used for ulcerated and uninjured tissue. 1 sample was used for intact tissue and organoid-derived RNA. The 'Ulcerated' samples represent C57BL/6 mice with ulcers and the 'Uninjured' samples represent the healthy controls (for "ulcerated" samples). The "Intact stomach tissue" and "Gastric organoids" samples are other types of samples that compared separately. "Gastric organoids" in this comparison are derived from "Intact stomach tissue".
Publication Title
The Development of Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) During Gastric Repair Is Absent in the Aged Stomach.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2000
Description
Purpose: we tested the hypothesis that Hltf deletion in placenta either caused or exacerbated neonatal hypoglycemia via Hif-1a regulation of nutrient transporters. Methods: Individual samples [1 term placenta/sample x 5 biological replicates for test and control littermate female mice = 10 total samples] were flash frozen and sent to Otogenetics Corp. (Norcross, GA) for RNA-seq assays. Paired-end 100 nucleotide reads were aligned to genomic assembly mm10 and analyzed using the platform provided by DNAnexus, Inc. (Mountain View, CA). Results: There was no measureable evidence of uteroplacental dysfunction or fetal compromise. Conclusion: Our study is the first to show only the truncated Hltf isoform is expressed in E18.5 term placenta, and we identified a functional link between alternative splicing of Hltf and immunosuppression at the feto-maternal interface. Overall design: Placental mRNA profiles of E18.5 term placenta from five wild type control and five Hltf null mouse samples were generated by deep sequencing by Illumina HiSeq2000/2500.
Publication Title
Alternative splicing of helicase-like transcription factor (Hltf): Intron retention-dependent activation of immune tolerance at the feto-maternal interface.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Rattus norvegicus
- 7 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a)
Description
Chronic alcohol ingestion changes the alveolar landscape. We used microarrays to characterize the change in mRNA expression following chronic alcohol ingestion in male Sprague Dawley rates (EtOH 36% of calories)
Publication Title
Chronic ethanol exposure alters the lung proteome and leads to mitochondrial dysfunction in alveolar type 2 cells.
Sample Metadata Fields
Sex, Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
DAP12 is a transmembrane protein, expressed as a disulfide-bonded homodimer and bears an immunoreceptor tyrosine-based activation motif (ITAM). DAP12 is broadly expressed in hematopoietic cells and associates with a variety of cell surface receptors in lymphoid and myeloid cells. Macrophages express several DAP12-associated receptors including triggering receptors expressed by myeloid cells (TREM)-1,2 and 3, myeloid DAP12-associating lectin (MDL)-1, CD200R like proteins CD200R3/R4 and CD300C/D/E .
Publication Title
Essential role of DAP12 signaling in macrophage programming into a fusion-competent state.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 2 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
In this experiment, total RNA was extracted from asynchronous population of L1210 cells and hybridized to Affymetrix 430A 2.0 arrays in order to obtain an expression profile of these cells. We have previously mapped the replication timing of the entire mouse genome in this cell line, using mouse CGH arrays (see E-MEXP-1022). We wanted to validate in our system the known correlation between early replication and expression and to analyze its extent. To this end, we have measured the expression in the same cell line (L1210 cells). Two biological replicates were hybridized to 2 identical microarrays. Expression levels were highly similar between the 2 replicates (r=0.98).
Publication Title
Global organization of replication time zones of the mouse genome.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
Gene expression profiling of macrophages derived from WT and Vdr deficient mice after stimulation with IFNgamma and/or 1alpha,25(OH)2D3
Publication Title
1alpha,25-Dihydroxyvitamin D3 is a potent suppressor of interferon gamma-mediated macrophage activation.
Sample Metadata Fields
No sample metadata fields
View Samples