GEO DataSets

(Submitter supplied) Several classes of small RNAs have been described, however to molecularly profile them require large numbers of cells. Here, we developed a method for single-cell small-RNA sequencing that we applied to naïve and primed human embryonic stem cells and to cancer cells. Single-cell profiling of microRNAs and fragments of tRNAs and snoRNAs revealed that, in particular, microRNAs have unrecognized potential to separate cell types and states.

Organism:

Homo sapiens; synthetic construct

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11154 GPL15228

539 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by array; Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL11180 GPL13112

26 Samples

Download data: CEL

(Submitter supplied) Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL13112

18 Samples

Download data: TXT

(Submitter supplied) Current RNA expression profiling methods rely on enrichment steps for specific RNA classes, thereby not detecting all RNA species in an unperturbed manner. We report strand-specific RNAome sequencing that determines expression of small and large RNAs from ribosomal RNA-depleted total RNA in a single sequence run. Since current analysis pipelines cannot reliably analyze small and large RNAs simultaneously, we developed TRAP, Total Rna Analysis Pipeline, a robust interface that is also compatible with existing RNA sequencing protocols. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11180

8 Samples

Download data: CEL

(Submitter supplied) Background: Small ncRNAs (sncRNAs) offer great hope as biomarkers of disease and response to treatment. This has been highlighted in the context of several medical conditions such as cancer, liver disease, cardiovascular disease, and central nervous system disorders, among many others. Here we assessed several steps involved in the development of an ncRNA biomarker discovery pipeline, ranging from sample preparation to bioinformatic processing. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15520 GPL16791

71 Samples

Download data: TXT

(Submitter supplied) Telomere length heterogeneity in various cell types including stem cells and cancer cells has been recognized. Cell heterogeneity also is found in pluripotent stem cells such as embryonic stem cells (ESCs). The implication and mechanisms underlying the heterogeneity remain to be defined. We have optimized a robust method that can simultaneously measure telomere length coupled with RNA-sequencing analysis (scT&R-seq) in the same human ES cell. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

121 Samples

Download data: TXT

(Submitter supplied) RNA structures are of crucial importance for biological function and gene regulation. Guanine (G)-rich sequences in RNA can assemble to form RNA G-quadruplex (rG4) structures; specific rG4s have been shown to regulate gene expression, and are associated with human diseases. However, no transcriptome-wide method has been reported to map rG4s, limiting our understanding of the rG4 structure and its relationship with function and regulation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: BED, BEDGRAPH, TDF

(Submitter supplied) Non-coding RNAs (ncRNAs) are essential components in cellular machineries for translation and splicing. In addition to their housekeeping functions, ncRNAs are involved in cell type-specific regulation of translation, mRNA stability, genome structure and accessibility. To decipher their functions in different cell types, a method to comprehensively quantify them in a sensitive manner is highly desirable. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: CSV, TXT

(Submitter supplied) We report here a new single-cell RNA-seq assay, Multiple Annealing and dC-Tailing based Quantitative single-cell RNA-seq (MATQ-seq), which provides the accuracy and sensitivity that enable the detection of transcriptional variations existing in single cells of the same type. We performed a systematic characterization of the technical noise using pool-and-split averaged single-cell samples and showed that the biological variations in single cells were observed with statistical significance.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

91 Samples

Download data: DAT, TXT

(Submitter supplied) This study presents a comparison of small RNA sequencing libraries generated from the same cell lines but using different sequencing platforms and protocols. The samples were analyzed and compared at the level of miRNAs expression and as a population of small RNAs derived from repetitive elements. Despite a good correlation between sequencing platforms, there are qualitative and quantitative variations in the results depending on the protocol used.

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

5 related Platforms

10 Samples

Download data: BED

(Submitter supplied) Single-cell mRNA sequencing (RNA-seq) methods have undergone rapid development in recent years, and transcriptome analysis of relevant cell populations at single-cell resolution has become a key research area of biomedical sciences. We here present single-cell mRNA 3-prime end sequencing (SC3-seq), a practical methodology based on PCR amplification followed by 3-prime-end enrichment for highly quantitative, parallel and cost-effective measurement of gene expression in single cells. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16288 GPL15907

98 Samples

Download data: TXT

(Submitter supplied) We applied ribosome profiling and RNA sequencing to examine gene expression regulation during oncogenic cell transformation. One model involves normal mammary epithelial cells (MCF10A) containing ER-Src. Treatment of such cells with tamoxifen rapidly induces Src, thereby making it possible to kinetically follow the transition between normal and transformed cells. The other model consists of three isogenic cell lines derived from primary fibroblasts in a serial manner (Hahn et al., 1999). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

36 Samples

Download data: TXT

(Submitter supplied) We use single molecule RNA FISH measurements of 26 genes in thousands of melanoma cells to provide an independent reference dataset to assess the performance of the DropSeq and Fluidigm single cell RNA sequencing platforms. We quantified the Gini coefficient, a measure of rare-cell expression variability, and find that the correspondence between RNA FISH and single cell RNA sequencing for Gini, unlike for mean, increases markedly with per-cell library complexity up to a threshold of ~2000 genes detected. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

801 Samples

Download data: TXT

(Submitter supplied) Small RNA molecules, including microRNAs (miRNAs), play critical roles in regulating pluripotency, proliferation and differentiation of embryonic stem cells. miRNA-offset RNAs (moRNAs) are similar in length to miRNAs, align to miRNA precursor (pre-miRNA) loci and are therefore believed to derive from processing of the pre-miRNA hairpin sequence. Recent next generation sequencing (NGS) studies have reported the presence of moRNAs in human neurons and cancer cells and in several tissues in mouse, including pluripotent stem cells. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10999

3 Samples

Download data: TXT

(Submitter supplied) Structure probing coupled with high-throughput sequencing holds the potential to revolutionize our understanding of the role of RNA structure in regulation of gene expression. Despite major technological advances, intrinsic noise and high coverage requirements greatly limit the applicability of these techniques. Here we describe a probabilistic modeling pipeline which accounts for biological variability and biases in the data, yielding statistically interpretable scores for the probability of nucleotide modification transcriptome-wide. more...

Organism:

Saccharomyces cerevisiae

Type:

Other

Platform:

GPL17342

4 Samples

Download data: SGR

(Submitter supplied) We used DART-seq to map m6A methylation of RNA in single HEK293T cells. We also used DART-seq to map m6A from bulk RNA from HEK293T cells. Using the 10X Genomics and SMART-seq2 platforms, we sequenced a total of 19,533 experimental and control cells using the 10X Genomics platform, and 1,471 experimental and control cells using SMART-seq2. We then used a Bullseye, a computational pipeline developed within the lab, to identify m6A sites from the C-to-U mutations in bulk and single-cell datasets. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1681 Samples

Download data: BED

(Submitter supplied) Soy-based diets have triggered the interest of the research community due to their beneficial effects on a wide variety of pathologies like breast and prostate cancer, diabetes, and atherosclerosis. However, the molecular details underlying these effects are far from being completely understood and several recent attempts have been made to elucidate the soy-induced liver transcriptome changes in different animal models. more...

Organism:

Mus musculus

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19057

6 Samples

Download data: XLS

(Submitter supplied) Soy-based diets have triggered the interest of the research community due to their beneficial effects on a wide variety of pathologies like breast and prostate cancer, diabetes, and atherosclerosis. However, the molecular details underlying these effects are far from being completely understood and several recent attempts have been made to elucidate the soy-induced liver transcriptome changes in different animal models. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL21810

6 Samples

Download data: TXT

(Submitter supplied) Clonal bacterial populations rely on transcriptional variation across individual cells to commit to specialized states that increase the population’s fitness. Such heterogeneous gene expression is implicated in fundamental microbial processes including sporulation, cell communication, detoxification, substrate utilization, competence, biofilm formation, and motility1. To identify specialized cell states and determine the processes by which they develop, isogenic bacterial populations need to be studied at the single cell level2,3. more...

Organism:

Bacillus subtilis; Escherichia coli; Clostridium perfringens

Type:

Expression profiling by high throughput sequencing

4 related Platforms

8 Samples

Download data: H5

(Submitter supplied) Obtaining high-quality omics data at the single-cell level from archived human tissue samples is crucial for gaining insights into cellular heterogeneity and pushing the field of personalized medicine forward. In this technical brief we present a comprehensive methodological framework for the efficient enzyme-free preparation of tissue-derived single cell suspensions and their conversion into single-cell miRNA sequencing libraries. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15520

33 Samples

Download data: TSV