GEO DataSets

(Submitter supplied) The transcriptome of single long-term self-renewing neuroepithelial-like stem cells (LT-NES) was studied in order to establish a baseline for investigations into modules of synergistically active transcription factors that determine developmental cell subpopulations

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

288 Samples

Download data: TAB

(Submitter supplied) To identify the “time-lapse” TF networks during B lineage commitment, we established multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system where virtually all cells became B cells within 6 days by simply withdrawing 4-OHT. In this study, single cell transcriptomic analysis at pre- and post-commitment was performed using the culture system. In addition, we also performed single cell RNA-seq analysis of B cell precursor populations (LMPP, CLP and pro-B cells) in murine bone marrow.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: MTX, TSV

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

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

68 Samples

Download data: WIG

(Submitter supplied) To identify the “time-lapse” TF networks during B lineage commitment, we established multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system where virtually all cells became B cells within 6 days by simply withdrawing 4-OHT. In this study, epigenomic analysis at multiple time points was performed using the culture system.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18480

24 Samples

Download data: WIG

(Submitter supplied) To identify the “time-lapse” TF networks during B lineage commitment, we established multipotent progenitors harboring a tamoxifen-inducible form of Id3, an in vitro system where virtually all cells became B cells within 6 days by simply withdrawing 4-OHT. In this study, transcriptome analysis at multiple time points was performed using the culture system.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18480

44 Samples

Download data: TXT

(Submitter supplied) Human pluripotent stem cells (hPSC) offer a unique cellular model to study the molecular details underpinning embryonic development. We profiled single-cell RNA-seq (scRNA-seq) on 957 single cells collected at 6 time points over a 30-day period of non-directed differentiation of human neural progenitor cells (NPC) generated from hESC. Computational and experimental analyses of this comprehensive data set enabled us to: 1) define distinct subpopulations of developing neurons and their specific gene expression patters; 2) elucidate alternative cell developmental trajectories within discrete time points of the differentiating populations; and 3) decipher gene regulatory networks and validated key regulators (transcription factors and lincRNAs) that dictate alternative cell fate specifications. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4556 Samples

Download data

(Submitter supplied) A brain consists of numerous distinct neurons arising from a limited number of progenitors, called neuroblasts in Drosophila. Each neuroblast makes a specific neuronal lineage. To unravel the transcriptional networks that underlie the development of distinct neuroblast lineages, we marked and isolated lineage-specific neuroblasts for RNA sequencing. We labeled particular neuroblasts throughout neurogenesis by activating a conditional neuroblast driver in specific lineages using various intersection strategies. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17275

22 Samples

Download data: TXT

(Submitter supplied) The gene expression circuitry that controls maintenance of normal liver physiology is poorly understood. Super-enhancers are known to contribute to mammalian cell identity. The injured liver loses normal functions, with concomitant decreased expression of key identity genes. Here, we identified core transcriptional regulators that are highly active in hepatocytes, using genome-wide analysis and hierarchical ordering of super-enhancer distribution. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

9 Samples

Download data: XLSX

(Submitter supplied) Detecting in vivo transcription factor (TF) binding is important for understanding gene regulatory circuitries. ChIP-seq is a powerful technique to empirically define TF binding in vivo. However, the multitude of distinct TFs makes genome-wide profiling for them all labor-intensive and costly. Algorithms for in silico prediction of TF binding have been developed, based mostly on histone modification or DNase I hypersensitivity data in conjunction with DNA motif and other genomic features. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

1 Sample

Download data: BED

(Submitter supplied) The retinal pigment epithelium (RPE) provides vital support to photoreceptor cells and its dysfunction is associated with the onset and progression of age-related macular degeneration (AMD). Surgical provision of RPE cells may ameliorate AMD and thus it would be valuable to develop sources of patient-matched RPE cells for this application of regenerative medicine. We describe here the generation of functional RPE-like cells from fibroblasts that represent an important step toward that goal. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platforms:

GPL570 GPL16043

20 Samples

Download data: CEL

(Submitter supplied) Adult neurogenesis in the murine dentate gyrus occurs in a specialized microenvironment that sustains the generation of neurons during life. To fully understand adult neurogenesis, it is essential to determine the neural stem cell (NSC) and progenitor developmental stages, their molecular determinants, and the niche cellular and molecular composition. We report on a single cell RNA sequencing study of the hippocampal niche, performed by isolating all the non-neuronal cell populations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

33 Samples

Download data: CSV, TSV

(Submitter supplied) Direct lineage reprogramming represents a remarkable conversion of cellular and transcriptome states. However, the intermediates through which individual cells progress are largely undefined. Here we used single cell RNA-seq at multiple time points to dissect direct reprogramming from mouse embryonic fibroblasts (MEFs) to induced neuronal (iN) cells. By deconstructing heterogeneity at each time point and ordering cells by transcriptome similarity rather than time we reconstructed a continuous reprogramming path. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19057 GPL13112

405 Samples

Download data: TXT

(Submitter supplied) The transcriptional programs that establish neuronal identity evolved to produce a rich diversity of neuronal cell types that arise sequentially during development. Remarkably, transient expression of certain transcription factors (TFs) can also endow non-neural cells with neuronal properties. To decipher the relationship between reprogramming factors and transcriptional networks that produce neuronal identity and diversity, we screened ~600 TF pairs and identified 76 that produce induced neurons (iNs) from fibroblasts. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19057

97 Samples

Download data: TXT

(Submitter supplied) Oscillatory gene expression is fundamental to mammalian development, but technologies to monitor expression oscillations are limited. We have developed a statistical approach called Oscope to identify and characterize the transcriptional dynamics of oscillating genes in single-cell RNA-seq data from an unsynchronized cell population. Applications to a number of data sets, include a single-cell RNA-seq data set of human embroyonic stem cells (hESCs), demonstrate advantages of the approach and also identify a potential artifact in the Fluidigm C1 platform.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

460 Samples

Download data: CSV

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

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL16791

65 Samples

Download data: TXT

(Submitter supplied) We tested a genome-scale artificial transcription factor (ATF) library in reprogramming mouse embryonic fibroblasts to induced pluripotent stem (iPS) cells. Three combinations of ATFs (C2, C3, and C4) could induce pluripotency when expressed with Sox2, Klf4, and c-Myc. The transcriptional profiles of ATF-induced iPS cells are similar to that of iPS cells induced with Oct4, Sox2, Klf4, and c-Myc and mouse embryonic stem cells, exhibiting up-regulation of pluripotency markers and down-regulation of fibroblast markers. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

22 Samples

Download data: CSV, TXT

(Submitter supplied) We tested various architectures of artificial transcription factors (ATFs) in HEK293 cells to test the contribution of the interaction domain, nuclear localization domain, size of DNA-binding domain, and activation domain. Then we made a genome-scale ATF library and tested it in reprogramming mouse embryonic fibroblasts to induced pluripotent stem (iPS) cells. Three combinations of ATFs (C2, C3, and C4) could induce pluripotency when expressed with Sox2, Klf4, and c-Myc. more...

Organism:

Mus musculus; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL17021

43 Samples

Download data: TXT

(Submitter supplied) To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss-of-heterozygosity in individual cells from single-cell RNA-sequencing data. By combining allele frequency and expression magnitude deviations, HoneyBADGER is able to infer the presence of subclone-specific alterations in individual cells and reconstruct subclonal architecture. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

174 Samples

Download data: TXT

(Submitter supplied) Single cell RNA seq and bioinformatic analysis is used to characterize myeloid differentiation to uncover novel transcriptional networks and key drivers of hematoipoietic development

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

47 Samples

Download data: TXT