GEO DataSets

(Submitter supplied) ESCs can adopt lineage-specific gene expression programs by stepwise exposure to defined factors, resulting in the generation of functional cell types. Bulk and single cell-based assays were employed to catalogue gene expression, histone modifications, chromatin conformation and accessibility transitions in ESC populations and individual cells acquiring a presomitic mesoderm fate and undergoing further lineage specification. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL21626 GPL17021 GPL24247

39 Samples

Download data: BED, CSV, H5, HIC, MTX, TBI, TSV, XLSX

(Submitter supplied) Single cell measurements of gene expression are providing new insights into lineage commitment, yet the regulatory changes underlying individual cell trajectories remain elusive. Here, we profiled chromatin accessibility in over 20,000 single nuclei across multiple stages of Drosophila embryogenesis. Our data reveal heterogeneity in the regulatory landscape prior to gastrulation that reflects anatomical position, a feature that aligns with future cell fate. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13304 GPL19132

4 Samples

Download data: BW, TXT

(Submitter supplied) Cell fate transitions involve integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of the genomic sequences that control the earliest steps of human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs) unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, and monomethylation of histone H3 at lysine 4 (H3K4me1). more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL9052

16 Samples

Download data: BED, TXT

(Submitter supplied) We have demonstrated that Meteor KO cells are associated with a global transcriptional reprogramming associated to a block of Mesendoderm specification. Meteor KO cells loses their developmental competence for Mesendoderm specification in pluripotency and are redirected to a neuroectoderm fate.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: TXT

(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:

GPL17021

36 Samples

Download data

(Submitter supplied) We mapped the enhancer and long non-coding transcriptional landscape during mesendoderm specification. Mesendodermal progenitors were sorted from differentiating ESCs according to Eomes expression. Enhancer usage was coordinated with mesendoderm-specific expression of key lineage-determining transcription factors. We demonstrated that many of these enhancers are associated with the expression of lncRNAs.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

24 Samples

Download data: BW

(Submitter supplied) We mapped the enhancer and long non-coding transcriptional landscape during mesendoderm specification. Mesendodermal progenitors were sorted from differentiating ESCs according to Eomes expression. Enhancer usage was coordinated with mesendoderm-specific expression of key lineage-determining transcription factors. We demonstrated that many of these enhancers are associated with the expression of lncRNAs.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

12 Samples

Download data: GTF, TXT

(Submitter supplied) We performed gene expression profiling on in vitro derived PGCs, undifferentiated ESCs, and somatic cells from the EB to examine germ cell expression in ESC-derived cells

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

10 Samples

Download data: CEL, CHP

(Submitter supplied) We investigated the genome-wide occupancy changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells of chromatin regulators and histone modifications.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17021

4 Samples

Download data: BW

(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

Platforms:

GPL17021 GPL13112

38 Samples

Download data: BED, BW

(Submitter supplied) We investigated the genome-wide occupancy changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells of chromatin regulators and histone modifications.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL13112

28 Samples

Download data: BED, BW

(Submitter supplied) We investigated the global gene expression changes in normal and Brg1-deleted mesoderm differentiation of mouse embryonic stem cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: BW

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

64 Samples

Download data: BED

(Submitter supplied) In this study, time-course transcriptome profiling of caidiomyocyte differentiation derived from human hESCs and hiPSCs was investigated. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes. The cells were collected for RNA-seq analysis at day0(undifferentiated cells) day2 (mesoderm), day4 (cardiac mesoderm) and day30 (cardiomyocytes) using Illumina HiSeq 2000 sequencer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

32 Samples

Download data: TXT

(Submitter supplied) In this study, time-course genome-wide chromatin accessibility of caidiomyocyte differentiation derived from human hESCs and hiPSCs was profiled. Two hiPSC lines (C15 and C20) and two hESC lines (H1 and H9) were differentiated to caidiomyocytes by ATAC-seq. The cells were collected for ATAC-seq at day 0(undifferentiated cells) day 2 (mesoderm), day 4 (cardiac mesoderm) and day 30 (cardiomyocytes).

Organism:

Homo sapiens

Type:

Other

Platform:

GPL11154

32 Samples

Download data: BED

(Submitter supplied) Single-cell technology was used to investigate dynamic transcriptional changes in the blastula and gastrula of Drosophila embryos. Cells from embryo of stages 5 to 9 were isolated and subjected to library construction. Mesoderm cells were labeled with mCD8-GFP utilizing the GAL/UAS system. PCA identified 12 unique cell clusters that represent the blastoderm, mesoderm, endoderm and ectoderm anlage, primordia, and a sampling of differentiating cell types. more...

Organism:

Drosophila melanogaster

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21306 GPL25244

3 Samples

Download data: H5

(Submitter supplied) Myogenic differentiation relies on Pax7 function. We used embryonic stem cells lacking functional Pax7 to follow its role in derivation of skeletal myoblasts. Microarray analysis allowed us to compare transcriptomes of undifferentiated and differentiating embryonic stem cells of two genotypes, i.e. Pax7+/+ and Pax7-/- at day 7 and 21 of culture.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL17400

18 Samples

Download data: CEL

(Submitter supplied) ESCs and NPCs are two setm cell types which rely on expression of the transcription factor Sox2. We profilled gene expression in ESCs and NPCs to correlate genome-wide Sox2 ChIP-Seq data in these cells with expression of putative targets

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL15722

6 Samples

Download data: CEL

(Submitter supplied) We analyzed the genome-wide binding of Sox2 and POU factor partner factors, Oct4 in ESCs (using published datasets PMID:18692474 and GSM307137, GSM307154, GSM307155) and Brn2 in NPCs. We found that Sox2 and Oct4 co-occupied a large subset of promoters and enhancers in ESCs, but that Sox2 and Brn2 co-occupy predominantly enhancers. Further, we overexpressed Brn2 in differentiating ESCs and showed that ectopic Brn2 recruited Sox2 to NPC-specific targets, resulting in skewed differentiation towards the neural lineage.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9250 GPL13112

30 Samples

Download data: WIG

(Submitter supplied) Human pluripotent stem cell- (hPSC)-derived skeletal muscle progenitors (SMP)—defined as PAX7-expressing cells with myogenic potential—can provide an abundant source of donor material for muscle stem cell therapy owing to the near-infinite replication potential of PSCs. As in vitro myogenesis is decoupled from in vivo timing and the 3D-embryo structure, it remains difficult to definitively characterize what stage or type of muscle is modeled in culture. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL20844

24 Samples

Download data: TXT