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Homo sapiens
7 Downloadable Samples
IlluminaGenomeAnalyzerII, IlluminaHiSeq2000
Description
Long noncoding RNAs (lncRNAs) have emerged as key players in different cellular processes and are required for diverse functions in vivo. However, fundamental aspects of lncRNA biology remain poorly characterized, including their subcellular localization, abundance and variation at a single cell resolution. Here, we used single molecule, single-cell RNA fluorescence in situ hybridization (RNA FISH) to survey 61 lncRNAs, chosen by properties such as conservation, tissue specific expression, and expression abundance, and to catalog their abundance and cellular localization patterns in three human cell types. Our lncRNAs displayed diverse sub-cellular localization patterns ranging from strictly nuclear localization to almost exclusive cytoplasmic localization, with the majority localized primarily in the nucleus. The low abundance of these lncRNAs as measured in bulk cell populations cannot be explained by high expression in a small subset of ''jackpot'' cells. Simultaneous analysis of lncRNAs and mRNAs from corresponding divergently transcribed loci showed that divergent lncRNAs do not present a distinct localization pattern and are not always co-regulated with their neighbor. Overall, our study highlights important differences and similarities between lncRNAs and mRNAs. The rich set of localization patterns we observe are consistent with a broad range of potential functions for lncRNA, and assists in hypothesis generation for mechanistic studies. Here we provide the RNA-Seq expression matrix, as well as RNA-Seq raw data, which we used for comparison with RNA FISH molecule counts. Overall design: We estimate FPKM of coding genes and lncRNAs across HeLa, human lung fibroblasts and human foreskin. This study includes data from human foreskin fibroblasts (hFF), human lung fibroblasts (hLF), and HeLa cells. An hFF sample (GSM1376178) and the hLF samples (GSM1376175-GSM1376177) were previously submitted and are available in GSE30554 as GSM759893 and GSM759890-GSM759892, respectively. The HeLa samples (GSM591670-GSM591671) were previously submitted and are available in GSE23316. The complete dataset representing: (1) the hFF Samples, including the re-analysis of the hFF Sample from GSE30554, (2) the re-analysis of the hLF Samples from GSE30554, and (3) the re-analysis of the HeLa Samples from GSE23316, is linked below as a supplementary file.
Publication Title
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution.
Sample Metadata Fields
No sample metadata fields
View Samples- Homo sapiens
- 98 Downloadable Samples
- IlluminaHiSeq2500, NextSeq500
Description
We performed single-cell and bulk transcriptome profiling in two different human cell lines. We performed single-cell RNA sequencing in live and fixed cells. Overall design: Single cell RNA sequencing of live and fixed cells, bulk RNA sequencing in two cell lines.
Publication Title
Single mammalian cells compensate for differences in cellular volume and DNA copy number through independent global transcriptional mechanisms.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 12 Downloadable Samples
- Illumina HiSeq 2000
Description
RNAseq analysis of YAP and Myc induced in quiescent and confluent 3T9 fibroblasts Overall design: RNAseq analysis of YAP and Myc induced in quiescent and confluent 3T9 fibroblasts
Publication Title
Transcriptional integration of mitogenic and mechanical signals by Myc and YAP.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 43 Downloadable Samples
- Illumina HiSeq 2000
Description
Tumors driven by activation of the transcription factor Myc generally show oncogene addiction. However, the gene-expression programs that depend upon sustained Myc activity in those tumors remain unknown. We have addressed this issue in a model of liver carcinoma driven by a reversible tet-Myc transgene, combining gene expression profiling with the mapping of Myc and RNA Polymerase II on chromatin. Switching off the oncogene in advanced carcinomas revealed that Myc is required for the continuous activation and repression of distinct sets of genes, constituting no more than half of those deregulated during tumor progression, and an even smaller subset of all Myc-bound genes. We further showed that a Myc mutant unable to associate with the co-repressor protein Miz1 is defective in the initiation of liver tumorigenesis. Altogether, our data provide the first detailed analysis of a Myc-dependent transcriptional program in a fully developed carcinoma, revealing that the critical effectors of Myc in tumor maintenance must be included within defined subsets (ca. 1,300 each) of activated and repressed genes. Overall design: RNAseq samples of control liver (n=11), tet-Myc tumors (n=16), tet-Myc tumors with short-term Myc inactivation (n=8), tet-MycVD tumors (n=11)
Publication Title
Identification of MYC-Dependent Transcriptional Programs in Oncogene-Addicted Liver Tumors.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 18 Downloadable Samples
Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Role of beta-arrestin2 in response to intermittent or continuous parathyroid hormone (PTH) treatment.
Publication Title
Beta-arrestin2 regulates parathyroid hormone effects on a p38 MAPK and NFkappaB gene expression network in osteoblasts.
Sample Metadata Fields
Sex, Age, Specimen part, Disease, Compound
View Samples- Homo sapiens
- 7 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Teratoma formation is the gold standard assay for testing the capacity of human stem cells to differentiate into all embryonic germ layers. Although widely used, little effort has been made to transform this qualitative assay into a quantitative one. Using gene expression data from a wide variety of cells, we created a gene scorecard representing tissues from all three germ layers as well as an extraembryonic tissue. A calculated grade using this gene list successfully distinguishes pluripotent stem cell-initiated teratomas from malignant tumors, thereby translating cell potency into a quantitative measure. This new methodology, named TeratoScore, thus assesses the pluripotency of human cells, and is easily performed using an open-source code. The new teratoma database also allowed us to examine the gene expression differences between tumors with a diploid karyotype and those initiated by aneuploid cells. We found that while teratomas originating from aneuploid cells pass the TeratoScore benchmark for pluripotency, they exhibit aberrant gene expression congruent with human chromosomal syndromes (such as Down syndrome). This gene expression signature is significantly different from that of teratomas originating from diploid cells, particularly in central nervous system-specific genes, suggesting aberrant teratomas may be beneficial for in vivo disease modeling. Teratoma formation followed by TeratoScore analysis can rapidly assess cell potency and allows comparison between different pluripotent cell lines.
Publication Title
TeratoScore: Assessing the Differentiation Potential of Human Pluripotent Stem Cells by Quantitative Expression Analysis of Teratomas.
Sample Metadata Fields
Cell line
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 5 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The second trimester fetal transcriptome can be assessed based on cell-free RNA found within the amniotic fluid supernatant. The objective of this study was to compare the suitability of two technologies for profiling the human fetal transcriptome: RNA-Seq and expression microarray. Comparisons were based on total numbers of gene detected, rank-order gene expression, and functional genomic analysis.
Publication Title
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome.
Sample Metadata Fields
Sex
View Samples- Homo sapiens
- 15 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The objective of this study was to identify the tissue expression patterns and biological pathways enriched in term amniotic fluid cell-free fetal RNA by comparing functional genomic analyses of term and second-trimester amniotic fluid supernatants.
Publication Title
Global gene expression analysis of term amniotic fluid cell-free fetal RNA.
Sample Metadata Fields
Sex
View Samples
GSE60403- Homo sapiens
- 16 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The objective of this study was to identify the tissue expression patterns and biological pathways enriched in term cord blood fetal RNA of obese women compared to lean
Publication Title
Assessing the fetal effects of maternal obesity via transcriptomic analysis of cord blood: a prospective case-control study.
Sample Metadata Fields
Specimen part
View Samples