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SRP068208
Homo sapiens
10 Downloadable Samples
IlluminaHiSeq2000
Description
In this study, we used a RNA-sequencing (RNA-seq) approach to analyze the whole transcriptomes of human primary Keratinocytes (KC) at undifferentiated stage and differentiated stage with and without FOXC1 knockdown. Each treatment condition have 2 or 3 replicates. 10 million reads were collected. A total of 8202 genes were designated as present (RPKM>5 in at least one sample). 635 genes were differentially expressed (FDR<0.01, P<0.000774201). FOXC1 knock-down significantly impaired keratinocytes differentiation process. Overall design: Proliferating foreskin normal human keratinocytes were seeded in 24 well-dishes and transfected with scrambled siRNA and FOXC1 siRNA duplexes. The following day, half of the wells were differentiated in vitro by increasing Ca2+ concentration in culture media from 0.06mM to 1.3 mM for 5 days. The other half wells of cells were cultured in 0.06mM CaCl2. Both undifferentiated and differentiated cells were harvested for total RNA extraction. RNA sequencing libraries were made using Illumina RNA sequencing library construction protocol. RNA libraries were sequenced by 100bp reads on Illumina Hi-seq 2000.
Publication Title
Forkhead Box C1 Regulates Human Primary Keratinocyte Terminal Differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 6 Downloadable Samples
- IlluminaHiSeq2000
Description
In this study, we used a RNA-sequencing (RNA-seq) approach to analyze the whole transcriptomes of human primary Keratinocytes (KC) at different differentiation stages. An average of 72.56 million reads were collected for each sample: 87.68% of the sequences could mapped to the human genome, and 66.70% of sequence mapped to known human genes. A total of 17,446 ± 220 genes were expressed during the course of differentiation. 1024 transcription factors (TF) and genes encoding TF binding proteins were detected during the course of differentiation were expressed during the course of KC differentiation. Overall design: Foreskin normal human keratinocytes were differentiated in vitro by increasing Ca2+ concentration in culture media from 0.06mM to 1.3 mM. Undifferentiated cells and cells under differentiation for 24 hrs, 48hrs, 72 hours, 96 hours and 120 hours were harvested for total RNA extraction. RNA sequencing libraries were made using eukaryotic long non-coding RNA sequencing library construction protocol. RNA libraries were deep sequenced by 100bp paired-reads on Illumina His-seq 2000.
Publication Title
Forkhead Box C1 Regulates Human Primary Keratinocyte Terminal Differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Using a mimic miR-200c was restored to an aggressive, Type 2 endometrial cancer cell line, Hec50
Publication Title
MicroRNA-200c mitigates invasiveness and restores sensitivity to microtubule-targeting chemotherapeutic agents.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 3 Downloadable Samples
- IlluminaHiSeq2000
Description
Micro (mi)RNAs are small non-coding RNAs with key regulatory functions. Recent advances in the field allowed researchers to identify their targets. However, much less is known regarding the regulation of miRNA themselves. The accumulation of these tiny regulators can be modulated at various levels during their biogenesis from the transcription of the primary transcript (pri-miRNA) to the stability of the mature miRNA. Here, we studied the importance of the pri-miRNA secondary structure for the regulation of mature miRNAs accumulation. To this end, we used the Kaposi’s sarcoma herpesvirus, which encodes a cluster of twelve pre-miRNAs. Using small RNA profiling and quantitative northern blot analysis, we measured the absolute amount of each mature miRNAs in different cellular context. We found that the difference in expression between the least and most expressed viral miRNA could be as high as 60-fold. Using high-throughput selective 2’-hydroxyl acylation analyzed by primer extension (hSHAPE), we then determined the secondary structure of the long primary transcript. We found that highly expressed miRNAs derived from optimally structured regions within the pri-miRNA. Finally, we confirmed the importance of the local structure by swapping stem-loops for highly and lowly expressed miRNAs, which resulted in a perturbed accumulation of the mature miRNA. Overall design: Examination of sRNA profiles in 3 independent B cell lines expressing KSHV miRNAs or infected with KSHV, without replicate
Publication Title
Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Cancer stemness in Wnt-driven mammary tumorigenesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 24 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
The Wnt/beta-catenin signalling pathway plays a central role in mammary stem cell homeostasis and in breast cancer. We employed the CD29hiCD24+ cell surface antigens to identify a subpopulation of mammary CSCs from Apc1572T/+, a mouse model for metaplastic breast adenocarcinoma, a subtype of triple-negative breast cancer in man. The MaCSCs are capable of recapitulating tumorigenesis when transplanted at low multiplicities in vivo, and of forming self-renewing organoids in vitro. Expression profiling of the different subpopulations sorted from normal and neoplastic mammary tissues revealed that the normal stem cell compartment is more similar to tumor cells than to their own differentiated progenies. Accordingly, Wnt signaling was found to be activated in the subpopulation encompassing normal mammary stem cells, though to a lesser degree than in the tumor cells. By comparing normal with cancer mouse mammary compartments, we were able to derive a MaCSC-specific signature composed of human orthologous genes able to predict poor survival, relapse and distant metastasis in human breast cancer. Finally, upon intravenous injection, only MaCSCs among the different tumor cell subpopulations are able to form metastatic lesions in a broad spectrum of anatomical sites. Overall, our data indicate that constitutive Wnt signaling activation interferes with mammary stem cell homeostasis leading to metaplasia and basal-like adenocarcinomas.
Publication Title
Cancer stemness in Wnt-driven mammary tumorigenesis.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
Cells grown in forced suspension culture mimic the early steps of metastasis. In order to determine what might be driving the ability of TNBC cells to survive in suspension, a global gene expression profiling experiment was performed. Human triple negative breast cancer (TNBC) cell line BT549 was grown in attached or forced suspension conditions for 24 hours, then RNA was harvested to look for changes in global gene expression.
Publication Title
Androgen Receptor Supports an Anchorage-Independent, Cancer Stem Cell-like Population in Triple-Negative Breast Cancer.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
Mediator is regarded a general co-activator of RNA-Polymerase II dependent transcription but not much is known about its function and regulation in mouse pluripotent embryonic stem cells (mESC). One means of controlling Mediator function is provided by binding of the Cdk8 module (Med12, Cdk8, Ccnc and Med13) to Mediator. Here we report that the Cdk8 module subunit Med12 operates together with PRC1 to silence developmental key genes in the pluripotent state. At the molecular level, PRC1 is required to assemble ncRNA containing Med12-Mediator complexes at promoters of repressed genes. In the course of cellular differentiation the H2A-ubiquitin binding protein Zrf1 abrogates PRC1-Med12 binding and facilitates the recruitment of Cdk8 into Mediator. Remodeling of the Mediator-associated protein complex converts Mediator into a transcriptional enhancer that mediates ncRNA-dependent activation of Polycomb target genes Overall design: RNAseq of pluripotent (control, shNMC, shRing1b, shMed12, shCdk8, shZrf1) and early differentiating (control, shNMC, shMed12, shCdk8, shZrf1) stem cells in triplicates. Control would be normal E14TG2A mESCs. shNMC refers to E14TG2A cells stably transfected with a short hairpin that has no mammalian targets (Non Mammalian Control). All the other samples are indeed stably transfected with short hairpins against the indicated genes.
Publication Title
Dual role of Med12 in PRC1-dependent gene repression and ncRNA-mediated transcriptional activation.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Constitutive expression of microRNA-150 in mammary epithelium suppresses secretory activation and impairs de novo lipogenesis.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Previoulsly expression profiling of the whole mammary gland across different stages of pregnancy and lactation has been performed on different strains of mice. Since mammary gland has both epithelial and stromal compartments, to specifically identify the genes involved in the transition from pregnancy to lactation a process termed as secretory activation, expression profiling of isolated mammary epithelial cells (MECs) from four CD1 mice each at Pregnancy day 14 (P14) and Lactation day 2 (L2) was performed in the current study.
Publication Title
Constitutive expression of microRNA-150 in mammary epithelium suppresses secretory activation and impairs de novo lipogenesis.
Sample Metadata Fields
Sex, Specimen part
View Samples