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SRP011993
Arabidopsis thaliana
6 Downloadable Samples
Illumina Genome Analyzer IIx
Description
Identification of microRNA expressed in Arabidopsis plants grown at different ambient CO2 concentrations and different ambient temperatures Overall design: Small RNA sequencing of Arabidopsis wild type ecotype Columbia (Col-0) rossette leaves at bolting stage grown at 430 ± 50ppm and 810 ± 50ppm CO2 concentrations and 22 ± 0.5oC and 28 ± 0.5oC temperatures
Publication Title
The effects of carbon dioxide and temperature on microRNA expression in Arabidopsis development.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 8 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The ability of male reproduction is seriously dependent on Sertoli cells. However, the mechanisms governing the functional integrity of Sertoli cells remained largely unexplored. Tyrosine phosphatase protein Shp2 is expressed in germ, Leydig and Sertoli cells of mice testes. But the physiological role of Shp2 in the spermatogenesis was not fully understood. Thus, we conditionally deleted Shp2 gene in Sertoli cells using two transgenic models, and demonstrated that Shp2 deficiency caused infertility, excessive differentiation of SSCs and abnormal BTB in mice. To further discover the underlying mechanism of Shp2 regulation, we collected the mRNA of testes from wild type or knockout mice at 16.5 fetal day, Postnatal 3 days, 1 weeks, 2 weeks, and then screened the gene expression.
Publication Title
Deletion of the tyrosine phosphatase Shp2 in Sertoli cells causes infertility in mice.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
To study the effect of PIAS1 on transcriptional regulation, we establishedstable PIAS1 shRNA knockdown cells in breast cancer cell line MDA-MB231.
Publication Title
PIAS1 regulates breast tumorigenesis through selective epigenetic gene silencing.
Sample Metadata Fields
Cell line, Treatment
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Androgenetic haploid embryonic stem cells produce live transgenic mice.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Haploid stem cells offer an easy-to-manipulate genetic system and therefore have great values for studies of recessive phenotypes. Here, we show that mouse androgenetic haploid ES (ahES) cell lines can be established by transferring sperm into enucleated oocyte. The ahES cells maintain haploidy and stable growth over 30 passages, express pluripotent markers, possess the ability to differentiate into all three germ-layers in vitro and in vivo, and contribute to germline of chimeras when injected into blastocysts. Although epigenetically distinct from sperm cells, the ahES cells can produce viable and fertile progenies after intracytoplasmic injection into mature oocytes. The oocyte injection procedure can also produce viable transgenic mice from genetically engineered ahES cells.
Publication Title
Androgenetic haploid embryonic stem cells produce live transgenic mice.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Haploid pluripotent stem cells, such as haploid embryonic stem cells (haESCs), facilitate the genetic study of recessive traits. In vitro, fish haESCs maintain haploidy in both undifferentiated and differentiated states, but whether mammalian haESCs can preserve pluripotency in the haploid state has not been tested. Here, we report that mouse haESCs can differentiate in vitro into haploid epiblast stem cells (haEpiSCs), which maintain an intact haploid genome, unlimited self-renewal potential, and durable pluripotency to differentiate into various tissues in vitro and in vivo. Mechanistically, the maintenance of self-renewal potential depends on the Activin/bFGF pathway. We further show that haEpiSCs can differentiate in vitro into haploid progenitor-like cells.
Publication Title
Durable pluripotency and haploidy in epiblast stem cells derived from haploid embryonic stem cells in vitro.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 38 Downloadable Samples
- NextSeq 500
Description
Regulatory T cells (Tregs) are a barrier to effective anti-tumor immunity. Neuropilin-1 (Nrp1) is required to maintain intratumoral Treg stability and function but is dispensable for peripheral immune homeostasis, Treg-restricted Nrp1 deletion in mice results in profound tumor resistant due to Treg functional fragility. Drivers of Treg fragility, the mechanistic basis of Nrp1 dependency, and the relevance of these processes for human cancer and immunotherapy remain unknown. NRP1 expression on human Tregs in melanoma and HNSCC was highly heterogeneous and correlated with prognosis. Using a mouse model of melanoma in which mutant Nrp1-deficient (Nrp1–/–) and wild type (WT) Tregs could be assessed in a competitive environment, we found that a high proportion of intratumoral Nrp1–/– Tregs produce interferon-? (IFN?), which in turn drove the fragility of surrounding WT Tregs, boosting anti-tumor immunity and facilitating tumor clearance. We also show that IFN?-induced Treg fragility is required for an effective response to PD1 immunotherapy, suggesting that cancer therapies promoting Treg fragility may be efficacious . Overall design: Tregs from B16 tumors and non-draining lymph nodes NDLN from WT, Nrp-1 deficient homozygous and heterozygous mice
Publication Title
Interferon-γ Drives T<sub>reg</sub> Fragility to Promote Anti-tumor Immunity.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina Genome Analyzer IIx
Description
The goal of this study was to investigate the role of intragenic CTCF in alternative pre-mRNA splicing through a combined CTCF-ChIP-seq and RNA-seq approach. CTCF depletion led to decreased inclusion of weak upstream exons. Overall design: CTCF ChIP-seq was performed in BJAB and BL41 B cell lines and normalized relative to Rabbit Ig control IP-seq reads. RNA-seq was performed in BJAB and BL41 cells transduced with shRNA against CTCF or RFP as a control, and in untransduced cells as well.
Publication Title
CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.
Sample Metadata Fields
Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Cyclic AMP response element binding protein (CREB) is known to play important roles in growth and drug resistance of various cancers. Here we show roles of inhibition of CREB1 on gene expression profile of malignant mesothelioma (MM) cells (Hmeso and H2373/PPMMill).
Publication Title
CREB-induced inflammation is important for malignant mesothelioma growth.
Sample Metadata Fields
Cell line
View Samples- Sus scrofa
- 78 Downloadable Samples
- Illumina HiSeq 2500
Description
To optimize the genome annotation, nine tissue and one pool RNA libraries (i.e. heart, liver, spleen, lung, kidney, muscle, fat, ovary, pool.) were constructed using the Illumina mRNA-spleeneq Prep Kit Overall design: We sequenced nine tissues and one pool using illumina Hiseq 2500 platform
Publication Title
Comprehensive variation discovery and recovery of missing sequence in the pig genome using multiple de novo assemblies.
Sample Metadata Fields
Age, Specimen part, Subject
View Samples