Filters
Organism
Technology
Platform
Sus scrofa
25 Downloadable Samples
NextSeq 500
Description
RNA-Seq of jejunum for 30 pigs with divergent feed efficiency phenotypes
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Sus scrofa
- 28 Downloadable Samples
- NextSeq 500
Description
RNASeq of hypothalamus for 30 pigs with divergent feed efficiency phenotypes
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Specimen part
View Samples- Homo sapiens
- 18 Downloadable Samples
Affymetrix Human Transcriptome Array 2.0 (hta20)
Description
Expansion for hematopoietic cells from umbilical cord blood is a strategy for use this cell source in clinic transplants, however, it is important to know about the genomic changes that can occur in expanded cells. In order to detect global expression profiles changes in hematopoietic stem and progenitors cells generated in vitro, we analyzed hematopoietics populations obtained by FACS in fresh from umbilical cord blood. HSC (fHSC) was defined as CD34+ CD38- CD71- CD45RA- Lin- and were cocultured with stromal cell line OP-9 plus FL, SCF, IL3, IL6, TPO, GMCSF and G-CSF by 7 days, after time we repurified HSC population by FACS using same immunophenotype (ivHSC). In other hand, fresh erythroid progenitors cells (fEPC) were identified as CD34+CD38+CD71+CD45RA- Lin- and fresh myeloid progenitors cells (fMPC) were identified as CD34+CD38+CD71-CD45RA+Lin-. In vitro progenitors cells (ivEPC and ivMPC) were obtained by culturing fHSC in Stemspan serum-free media plus SCF, TPO, IL6, FL and IL3 by 10 days, after time cells were repurified by FACS using same immunophenotype for fresh progenitors. In vitro generated cells were compared with their corresponding fresh population cells.
Publication Title
Functional Integrity and Gene Expression Profiles of Human Cord Blood-Derived Hematopoietic Stem and Progenitor Cells Generated In Vitro.
Alternate Accession IDs
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- NextSeq 550, NextSeq 500
Description
Differential expression analysis of different tissues from wild type and ApoE mutant mice
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Cell line
View Samples- Homo sapiens
- 96 Downloadable Samples
- Affymetrix HT HG-U133+ PM Array Plate (hthgu133pluspm)
Description
Human immature dendritic cells derived from monocytes were activated to become mature dendritic cells by exposure to platebound Collagen I or Collagen. The importance of OSCAR-signalling was evaluated by pre-incubating the immature dendritic cells with an inhibitory monoclonal antibody to the OSCAR receptor, or an isotype control. As a positive control, immature dendritic cells were activated by using LPS. The set-up was examined at 4 hours and 20 hours to evaluate early and late effects of OSCAR signalling.
Publication Title
Collagen induces maturation of human monocyte-derived dendritic cells by signalling through Osteoclast Associated Receptor
Alternate Accession IDs
None
Sample Metadata Fields
Specimen part, Subject, Compound, Time
View Samples- Mus musculus
- 36 Downloadable Samples
- Illumina HiSeq 2000
Description
Recent studies suggest vitamin D deficiency is associated with chronic lung diseases such as asthma and chronic obstructive pulmonary disease. Each of these are characterised by airway hyperresponsiveness (AHR) and airway remodeling, the latter characterized by increased airway smooth muscle (ASM) mass. In this study we investigated the biological mechanisms underlying increased ASM mass and AHR due to vitamin D deficiency via RNA-seq transcriptome analysis of female BALB/c mice at 8 weeks of age.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 36 Downloadable Samples
- Illumina HiSeq 2500
Description
RNA expression in adipose and skin from women with polycystic ovary syndrome (PCOS) was examined using RNA sequencing (Illumina HiSeq 50 cycle single-read sequencing) as a function of the genotype at 16 PCOS genetic risk variants. We hypothesized that the tissue expression pattern in adipose and skin would help identify candidate genes and pathways that could provide insight into the underlying mechanism for risk at these loci.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part
View Samples
SRP064894- Homo sapiens
- 30 Downloadable Samples
- IlluminaHiSeq2500
Description
High-throughput sequencing of RNA (RNA-Seq) in human cancer shows remarkable potential to simultaneously identify expression levels of protein-coding genes and long non-coding RNAs (lncRNAs). We performed RNA-Seq to investigate expression level of lncRNAs and protein-coding genes in 30 esophageal samples, including 15 esophageal squamous cell carcinoma (ESCC) tissue samples and 15 paired non-tumor tissues. We further developed an integrative bioinformatics method, denoted URW-LPE (for unsupervised random walk with each dysregulated lncRNA/PCG), to identify key functional lncRNAs that regulate expression of downstream protein-coding genes in ESCC. By this method, multiple known cancer and novel potentially functional lncRNAs were effectively identified. Quantitative reverse-transcription PCR was performed to confirm the lncRNA expression level of eight novel functional lncRNAs in an additional 120 paired ESCC patient samples. Finally, we characterized lncRNA625 as a novel ESCC regulator of cell proliferation, invasion and migration. Moreover, we identified E1A-binding protein p300 (EP300) as playing a key role in executing lncRNA625-induced transcriptional responses. These findings establish the utility of integrative bioinformatics analyses of RNA-Seq to identify cancer-associated functional lncRNAs.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
No sample metadata fields
View Samples- Rattus norvegicus
- 20 Downloadable Samples
- Affymetrix Rat Genome U34 Array (rgu34a), Affymetrix Rat Genome U34 Array (rgu34b)
Description
We report a comprehensive large-scale expression profiling analysis of mammalian male germ cells undergoing mitotic growth, meiosis and gametogenesis using High Density Oligonucleotide Microarrays and highly enriched cell populations. Among 11955 rat loci investigated, 1268 were identified as differentially transcribed in germ cells at subsequent developmental stages as compared to total testis, somatic Sertoli cells as well as brain and skeletal muscle controls. The loci were organized into four expression clusters that correspond to somatic, mitotic, meiotic and post-meiotic cell types. This work provides information about expression patterns of approximately 200 genes known to be important during male germ cell development. Approximately 40 of those are included in a group of 121 transcripts for which we report germ cell expression and lack of transcription in three somatic control cell types. Moreover, we demonstrate the testicular expression and transcriptional induction in mitotic, meiotic and/or post-meiotic germ cells of 293 as yet uncharacterized transcripts some of which are likely to encode factors involved in spermatogenesis and fertility. This group also contains numerous potential germ cell specific targets for innovative contraceptives. A graphical display of the data is conveniently accessible through the GermOnline database at <a href="http://www.germonline.org" target="_blank">http://www.germonline.org</a>.
Publication Title
Expression profiling of mammalian male meiosis and gametogenesis identifies novel candidate genes for roles in the regulation of fertility.
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
CH causes perivascular inflammation, enhanced pulmonary arterial constriction and remodeling leading to the development of pulmonary hypertension. Pulmonary hypertension is a debilitating disease with a high mortality rate. CH develops in patients with chronic obstructive pulmonary disease (COPD), sleep apnea or people living at high altitude. Both COPD and sleep apnea are very prevalent and pulmonary hypertension develops in a large % of COPD and sleep apnea patients. The molecular mechanisms that underlie the development of CH-induced pulmonary hypertension are far from clear. We have previously demonstrated that CH activates the Ca2+/calcineurin-regulated transcription factor NFATc3 in PASMC and that NFATc3 is required for CH-induced pulmonary hypertension in mice. Although this work was the first to identify a role for this transcription factor in an experimental model of pulmonary hypertension, since a conventional whole animal KO was used it is unknown if PASMC NFATc3 contributes to CH-induced PH. Furthermore, the genes regulated by NFATc3 in PASMC under control and CH conditions are largely unknown.
Publication Title
No associated publication
Alternate Accession IDs
None
Sample Metadata Fields
Sex, Age, Specimen part, Treatment
View Samples