Filters
Technology
Platform
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
- 26 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Whole exome sequencing identified frequent driver mutations in a series of paediatric glioblastomas
Publication Title
Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma.
Sample Metadata Fields
Sex, Age, Disease, Disease stage
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- Homo sapiens
- 46 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Glioblastoma (GBM) is an incurable brain tumor carrying a dismal prognosis, which displays considerable heterogeneity. We have recently identified recurrent H3F3A mutations affecting two critical positions of histone H3.3 (K27, G34) in one-third of pediatric GBM. Here we show that each of these H3F3A mutations defines an epigenetic subgroup of GBM with a distinct global methylation pattern, and are mutually exclusive with IDH1 mutation (characterizing a CpG-Island Methylator Phenotype (CIMP) subgroup). Three further epigenetic subgroups were enriched for hallmark genetic events of adult GBM (EGFR amplification, CDKN2A/B deletion) and/or known transcriptomic signatures. We also demonstrate that the two H3F3A mutations give rise to GBMs in separate anatomic compartments, with differential regulation of OLIG1/2 and FOXG1, possibly reflecting different cellular origins.
Publication Title
Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma.
Sample Metadata Fields
Sex
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