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SRP074763
Mus musculus
9 Downloadable Samples
Illumina HiSeq 2500
Description
Cultured pluripotent stem cells are a cornerstone of regenerative medicine due to their ability to give rise to all cell types of the body. While pluripotent stem cells can be propagated indefinitely in vitro, pluripotency is paradoxically a very transient state in vivo, lasting 2-3 days around the time of blastocyst implantation. The exception to this rule is embryonic diapause, a reversible state of suspended development triggered by unfavorable conditions. Diapause is a strategy widely employed across the animal kingdom, including in mammals, but its regulation remains poorly understood. Here we report that inhibition of mechanistic target of rapamycin (mTor), a major nutrient sensor and promoter of growth, induces reversible pausing of mouse blastocyst development and allows their prolonged culture ex vivo. Paused blastocysts remain pluripotent and competent to give rise to embryonic stem (ES) cells and mice. We show that both natural diapause blastocysts in vivo and paused blastocysts ex vivo display pronounced reductions in mTor activity, translation and transcription. In addition, pausing can be induced directly in cultured ES cells and sustained for weeks in the absence of cell death or deviations from cell cycle distributions. We show that paused ES cells remain pluripotent, display a remarkable global suppression of transcription, and maintain a gene expression signature of diapaused blastocysts. These results allow for the first time the sustained suspension of development of a mammalian embryo in the laboratory, and shed light on the regulation of diapause and the origins of ES cells. Our findings have important implications in the fields of assisted reproduction, regenerative medicine, cancer, metabolic disorders and aging. Overall design: Examination of RNA expression profiles of embryonic stem cells in serum, 2i and paused states by RNA-seq
Publication Title
Inhibition of mTOR induces a paused pluripotent state.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
Transposable elements make up nearly half of mammalian genomes, yet are generally described as 'junk DNA' or genome parasites. The LINE1 retrotransposon is the most abundant class and is thought to be deleterious for cells, but it is paradoxically expressed at high levels during early development. Here, we report that LINE1 plays essential roles in mouse embryonic stem (ES) cells and pre-implantation embryos. In ES cells, LINE1 acts as a nuclear RNA scaffold that recruits Nucleolin and Kap1/Trim28 to repress Dux, the master activator of a gene expression program specific to the 2-cell stage. In parallel, LINE1 RNA mediates binding of Nucleolin and Kap1 to rDNA, thereby promoting rRNA synthesis and ES cell self-renewal. In embryos, LINE1 RNA is required for silencing of Dux, proper synthesis of rRNA and exit from the 2-cell stage. These results reveal an essential partnership between nuclear LINE1 RNA and chromatin factors in the regulation of transcription, developmental potency and ES cell self-renewal. Overall design: 3 replicates each of E14 ES cells two days after nucleofection with Lissaminated ASOs - RC (control) or LINE1, purified according to Lissamine+ using flow cytometry then lysed for RNA extraction and library generation (6 samples total)
Publication Title
A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 4 Downloadable Samples
- Illumina HiSeq 2500
Description
The pluripotent mammalian epiblast undergoes unusually fast cell proliferation. This rapid growth is expected to generate a high transcriptional demand, but the underlying mechanisms remain unknown. We report that the chromatin remodeler Chd1, which binds the activating histone mark H3K4me3 and is associated with transcription, is required for development of the mouse epiblast. Chd1-/- embryos exhibit proliferation defects and increased apoptosis, are smaller than controls by E5.5, and fail to grow, become patterned or gastrulate. We show that Chd1-/- ES cells have a self-renewal defect and a genome-wide reduction in transcriptional output that is associated with losses in RNA Pol II elongation at growth-promoting genes, including ribosomal proteins. We also report that Chd1 directly regulates ribosomal RNA transcription and that both Chd1-/- epiblast cells in vivo and ES cells in vitro express significantly lower levels of ribosomal RNA. Single cell analyses reveal abnormal nucleolar morphology in mutants in vivo and in vitro. These data indicate that Chd1 promotes a globally elevated transcriptional output required to sustain the distinct rapid growth of the mouse epiblast. Overall design: Cell-number normalized RNA-seq from wild-type and Chd1-/- mouse embryonic stem cells.
Publication Title
Chd1 is essential for the high transcriptional output and rapid growth of the mouse epiblast.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 15 Downloadable Samples
Affymetrix Mouse Clariom S Array (clariomsmouse)
Description
Failures to produce neutralizing antibodies upon HIV-1 infection result in part from B cell dysfunction due to unspecific B cell activation. How HIV-1 affects antigen-specific B cell functions remains elusive. Using an adoptive transfer mouse model and ex vivo HIV infection of human tonsil tissue we found that expression of the HIV-1 pathogenesis factor NEF in CD4 T cells undermines their helper function and impairs cognate B cell functions including mounting of efficient specific IgG responses. NEF interfered with T cell help via a specific protein interaction motif that prevents polarized cytokine secretion at the T cell - B cell immune synapse. This interference reduced B cell activation and proliferation and thus disrupted germinal center formation and affinity maturation. These results identify NEF as a key component for HIV-mediated dysfunction of antigen-specific B cells. Therapeutic targeting of the identified molecular surface in NEF will facilitate host control of HIV infection.
Publication Title
HIV-1 infection of CD4 T cells impairs antigen-specific B cell function.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Estrogen receptor-{alpha} (ER{alpha}) and its ligand estradiol play critical roles in breast cancer growth and are important therapeutic targets for this disease. Using chromatin immunoprecipitation (ChIP)-on-chip, ligand-bound ER{alpha} was recently found to function as a master transcriptional regulator via binding to many cis-acting sites genome-wide. Here, we used an alternative technology (ChIP cloning) and identified 94 ER{alpha} target loci in breast cancer cells. The ER{alpha}-binding sites contained both classic estrogen response elements and nonclassic binding sequences, showed specific transcriptional activity in reporter gene assay, and interacted with the key transcriptional regulators, including RNA polymerase II and nuclear receptor coactivator-3. The great majority of the binding sites were located in either introns or far distant to coding regions of genes. Forty-three percent of the genes that lie within 50 kb to an ER{alpha}-binding site were regulated by estradiol. Most of these genes are novel estradiol targets encoding receptors, signaling messengers, and ion binders/transporters. mRNA profiling in estradiol-treated breast cancer cell lines and tissues revealed that these genes are highly ER{alpha} responsive both in vitro and in vivo. Among estradiol-induced genes, Wnt11 was found to increase cell survival by significantly reducing apoptosis in breast cancer cells. Taken together, we showed novel genomic binding sites of ER{alpha} that regulate a novel set of genes in response to estradiol in breast cancer. Our findings suggest that at least a subset of these genes, including Wnt11, may play important in vivo and in vitro biological roles in breast cancer.
Publication Title
Novel estrogen receptor-alpha binding sites and estradiol target genes identified by chromatin immunoprecipitation cloning in breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 11 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
LRH-1 drives colon cancer cell growth by repressing the expression of the CDKN1A gene in a p53-dependent manner.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 9 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Liver receptor homologue 1 (LRH-1) is an orphan nuclear receptor which has been implicated in the growth and development of breast, pancreatic and colorectal cancers (CRC). In order to identify novel LRH-1-regulated genes in CRC cells, we performed gene expression profiling following siRNA-mediated LRH-1 silencing in the CRC cell line HCT116.
Publication Title
LRH-1 drives colon cancer cell growth by repressing the expression of the CDKN1A gene in a p53-dependent manner.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 2 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
Liver receptor homologue 1 (LRH-1) is an orphan nuclear receptor which has been implicated in the growth and development of breast, pancreatic and colorectal cancers (CRC). In order to identify novel LRH-1-regulated genes in CRC cells, we performed gene expression profiling following siRNA-mediated LRH-1 silencing in the CRC cell line HT29.
Publication Title
LRH-1 drives colon cancer cell growth by repressing the expression of the CDKN1A gene in a p53-dependent manner.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 22 Downloadable Samples
- IlluminaHiSeq2500
Description
Estrogen receptor-a (ERa) is an important driver of breast cancer and is the target for hormonal therapies, anti-estrogens and drugs that limit estrogen biosynthesis (aromatase inhibitors). Mutations in the ESR1 gene identified in metastatic breast cancer provide a potential mechanism for acquired resistance to hormone therapies. We have used CRISPR-Cas9 mediated genome editing in the MCF-7 breast cancer cell line, generating MCF-7-Y537S. MCF-7-Y537S cells encode a wild-type (tyrosine 537) and a mutant (serine 537) allele. Growth of the line is estrogen-independent and expression of ERa target genes is elevated in the absence of estrogen. ER ChIP-seq was carried out to map global ERa binding sites in the presence and absence of estrogen. RNA-seq following estrogen treatment was used for gene expression analysis. We show that expression of ER target genes and ER recruitment to ER binding regions is similar in MCF-7 and MCF-7-Y537S cells, except that ER recruitment to DNA and expression of ER target genes is frequently elevated in the absence of estrogen. Overall design: Hormone depleted MCF7 Luc or Y537S cells were treated with 10nM E2 or ethanol, as vehicle control, for 8 hours, with 3 replicates (2 replicates for Y537S + E2). RNA-seq was carried out using Illumina Hiseq 2500.
Publication Title
Genomic modelling of the ESR1 Y537S mutation for evaluating function and new therapeutic approaches for metastatic breast cancer.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Gonadal sex determining (GSD) genes that initiate fetal ovarian and testicular development and differentiation are expressed in the cells of the urogenital ridge that differentiate as somatic support cells (SSCs), i.e., granulosa cells of the ovary and Sertoli cells of the testis. To identify potential new mammalian GSD genes, we analyzed the gene expression differences between XX and XY SSCs cells isolated from the gonads of embryonic day (E) 13 mouse fetuses carrying an EGFP reporter transgene expressed specifically in SSCs. In addition, genome wide expression differences between XX and XY E13 whole gonads were examined. Newly identified differentially expressed transcripts are potential GSD genes involved in unexplained human sex reversal cases.
Publication Title
Transcriptional profile of mouse pre-granulosa and Sertoli cells isolated from early-differentiated fetal gonads.
Sample Metadata Fields
No sample metadata fields
View Samples