Filters
Technology
Platform
Mus musculus
21 Downloadable Samples
Illumina HiSeq 2500
Description
The prevailing dogma that approximately 50% of our genome is “junk” DNA composed of transposable elements and retroviral insertions has recently been challenged. It has become evident that our genome has taken advantage of these transposable elements and uses them as a source of DNA to generate novel genes, which subsequently allow the organism to evolve. This process is termed “domestication of transposable elements” and the majority of these genes have been found to be essential for the existence of the organism. One of these developmentally essential domesticated genes: Peg10 (paternally expressed gene 10), was derived from a Ty3/gyspy LTR retrotransposon, yet lost its ability to transpose due to mutational events during its domestication. Remarkably, Peg10 has successfully maintained its Gag and Pol-like domains for millions of years. Peg10 orthologues are expressed in eutherian mammals and are essential for placentogenesis. To address the functional mechanisms of Peg10 we studied it in Trophoblast Stem Cells (TSCs). We find that the Gag of Peg10 is fully active: it promotes budding of vesicles, akin to the viral counterpart that catalyzes the budding of viruses. TSCs, deleted for Peg10, fail to differentiate into placental lineages, underscoring a critical role in lineage specification. This paper discusses our efforts to characterize the contents of Peg10 vesicles and whether such vesicles regulate lineage specification. Overall design: RNA was extracted from following genotypes - wildtype TSCs (WT_TSC), Peg10 knockout TSCs (KO_TSC), wildtype TSCs differentiated in 20% oxygen (WT_TSC_diff), Peg10 knockout TSCs differentiated in 20% oxygen (KO_TSC_diff), wildtype TSCs differentiated in 2% oxygen (WT_diff_2O2),and Peg10 knockout TSCs differentiated in 2% oxygen (KO_diff_2O2). Cells are kept in the pluripotent state by growing them on CellStart/Fgf4/Heparin. The cells were differentiated in two different conditions: 20% oxygen and 2% oxygen. The samples were collected at 10th day following differentiation. Cells are harvested and RNA is isolated using the Qiagen RNeasy kit. RT-PCR was performed for several differentiation markers to validate the success of the assay.
Publication Title
The Gag protein PEG10 binds to RNA and regulates trophoblast stem cell lineage specification.
Sample Metadata Fields
Specimen part, Subject
View Samples- Drosophila melanogaster
- 28 Downloadable Samples
- Illumina HiSeq 2000
Description
We report the identification of Rnase R resistent stable intronic sequence RNAs (sisRNAs) in Drosophila. Overall design: RNA was obtained from 0-2 hr embryos and subjected to deep sequencing. ---------------------------------------- Authors state "We screened by manual inspection on the genome browser after mapping the reads to the genome" and "We managed to obtain 6 candidates with this approach".
Publication Title
Maternally Inherited Stable Intronic Sequence RNA Triggers a Self-Reinforcing Feedback Loop during Development.
Sample Metadata Fields
Subject
View Samples- Homo sapiens
- 10 Downloadable Samples
Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
E2 exposure significantly decreased peak viral titer in hNECs from female donors. We used microarray analyses to identify global gene expression patterns between E2 and vehicle exposed hNECs from female donors
Publication Title
Estrogenic compounds reduce influenza A virus replication in primary human nasal epithelial cells derived from female, but not male, donors.
Sample Metadata Fields
Sex, Specimen part, Treatment
View Samples- Drosophila melanogaster
- 6 Downloadable Samples
- Illumina HiSeq 2000
Description
We report the identification of stable intronic sequence RNAs (sisRNAs) in Drosophila. Overall design: RNA was obtained from unfertilized eggs and subjected to deep sequencing.
Publication Title
Generation of Drosophila sisRNAs by Independent Transcription from Cognate Introns.
Sample Metadata Fields
Subject
View Samples
SRP058703- Drosophila melanogaster
- 1 Downloadable Sample
- Illumina HiSeq 2000
Description
We report the identification of stable intronic sequence RNAs (sisRNAs) in Drosophila. Overall design: RNA was obtained from 0-2 hr embryos and subjected to deep sequencing.
Publication Title
Stable intronic sequence RNAs have possible regulatory roles in Drosophila melanogaster.
Sample Metadata Fields
Subject
View Samples- Mus musculus
- 9 Downloadable Samples
- Affymetrix Mouse Expression 430A Array (moe430a)
Description
To understand the developing striatum, key genes during development were identified using microarray analsyis tha could be considered as marker of medium spiny neurons. The ages studied is at peak striatal neurogenesis.
Publication Title
FoxP1 marks medium spiny neurons from precursors to maturity and is required for their differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 768 Downloadable Samples
- Illumina HiSeq 2000
Description
This study was conducted to determine heterogeneity of cancer-associated fibroblasts (CAFs) in mammary tumors, by unsupervised analysis of single cell transcriptomes. Overall design: 768 single EpCAM-, CD45-, CD31- NG2- fibroblasts were isolated from mammary tumors of two 14 week old MMTV-PyMT mice. The cells were sequenced following the Smart-Seq2 protocol (Picelli et al. Nature Methods 2013).
Publication Title
Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.
Sample Metadata Fields
Age, Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 8 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The generation of induced pluripotent stem (iPS) cells 1-4 has spawned unprecedented opportunities for investigating the molecular logic that underlies cellular pluripotency and reprogramming, as well as for obtaining patient-specific cells for future clinical applications. However, both prospects are hampered by the low efficiency of the reprogramming process. Here, we show that juvenile human primary keratinocytes can be efficiently reprogrammed to pluripotency by retroviral transduction with Oct4, Sox2, Klf4 and c-Myc. Keratinocyte-derived iPS (KiPS) cells appear indistinguishable from human embryonic stem (hES) cells in colony morphology, growth properties, expression of pluripotency-associated transcription factors and surface markers, as well as in vitro and in vivo differentiation potential. Notably, keratinocyte reprogramming to pluripotency is, at least, 100-fold more efficient and 2-fold faster than that of fibroblasts. This increase in reprogramming efficiency allowed us to expand the practicability of the technology and to generate KiPS cells from single plucked hairs from adult individuals.
Publication Title
Efficient and rapid generation of induced pluripotent stem cells from human keratinocytes.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 3 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Transcription-dependent generation of a specialized chromatin structure at the TCRβ locus.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 37 Downloadable Samples
- Illumina HiSeq 2500
Description
We performed RNA-seq on 42 meningioma samples isolated from human patients to characterize the transcriptome of these tumors Overall design: Poly A selected RNA-seq from 42 meningioma samples
Publication Title
Comprehensive Molecular Profiling Identifies FOXM1 as a Key Transcription Factor for Meningioma Proliferation.
Sample Metadata Fields
Specimen part, Subject
View Samples