GEO DataSets

(Submitter supplied) Tbx3 regulates liver development in the mouse, but it's role in human liver development is unclear. We generated TBX3 knockout pluripotent stem cell lines and found that liver differentiation is also impaired in humans. Interestingly we noted expression of pancreas-specific genes during the liver differentiation in the TBX3 knockout line. To further investigate this phenomenon, we performed RNA-seq on cells at the hepatoblast stage of the liver differentiation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL20301

22 Samples

Download data: BIGWIG

(Submitter supplied) Tbx3 regulates liver development in the mouse, but it's role in human liver development is unclear. We generated TBX3 knockout pluripotent stem cell lines and found that liver differentiation is also impaired in humans. Interestingly we noted expression of pancreas-specific genes during the liver differentiation in the TBX3 knockout line. To further investigate this phenomenon, we performed ATAC-seq on cells at the hepatoblast stage of the liver differentiation. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: BIGWIG

(Submitter supplied) Tbx3 regulates liver development in the mouse, but it's role in human liver development is unclear. We generated TBX3 knockout pluripotent stem cell lines and found that liver differentiation is also impaired in humans. Interestingly we noted expression of pancreas-specific genes during the liver differentiation in the TBX3 knockout line.To further investigate this phenomenon, we performed RNA-seq on cells from two stages of the pancreatic differentation. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) Tbx3, a member of the T-box family, plays important roles in development, stem cells, nuclear reprogramming and cancer. Loss of Tbx3 induces differentiation in mouse embryonic stem cells (mESCs). However, we show that mESCs exist in an alternate stable pluripotent state in the absence of Tbx3. In-depth transcriptome analysis of this mESC state reveals Dppa3 as a direct downstream target of Tbx3. Also Tbx3 facilitates the cell fate transition from pluripotent cells to mesoderm progenitors by directly repressing Wnt pathway members required for differentiation. more...

Organism:

Mus musculus

Type:

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

Platforms:

GPL13112 GPL9250

53 Samples

Download data: BED, BEDGRAPH, BIGWIG, TXT

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16686 GPL18460

12 Samples

Download data: CEL

(Submitter supplied) We performed ChIP-seq of PDX1 and H3K27ac on XM001 cells at PP stage

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18460

8 Samples

Download data: BED

(Submitter supplied) Objective: Homozygous loss-of-function mutations in the gene coding for the homeobox transcription factor (TF) PDX1 leads to pancreatic agenesis, whereas heterozygous mutations can cause Maturity-Onset Diabetes of the Young 4 (MODY4). Although the function of Pdx1 is well studied in pre-clinical models during insulin-producing β-cell development and homeostasis, it remains elusive how this TF controls human pancreas development by regulating a downstream transcriptional program. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

4 Samples

Download data: CEL

(Submitter supplied) Induced pluripotent stem (iPS) cells can be obtained through the introduction of defined factors into somatic cells. The combination of Oct4, Sox2 and Klf4 (OSK) constitutes the minimal requirement for generating iPS cells from mouse embryonic fibroblasts (MEFs). Through the genomic analyses of ESC genes that have roles in pluripotency and fusion-mediated somatic cell reprogramming, we identified Tbx3 as a transcription factor that significantly improves the quality of iPS cells. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9250

2 Samples

Download data: BED

(Submitter supplied) Induced pluripotent stem (iPS) cells can be obtained through the introduction of defined factors into somatic cells. The combination of Oct4, Sox2 and Klf4 (OSK) constitutes the minimal requirement for generating iPS cells from mouse embryonic fibroblasts (MEFs). These cells are thought to resemble embryonic stem cells (ESCs) based on global gene expression analyses; but, few studies have tested their ability and efficiency in contributing to chimerism, colonization of germ tissues, and most importantly, germ-line transmission and life-birth from iPS cells produced with tetraploid complementation. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6103

36 Samples

Download data: TXT

(Submitter supplied) ATAC-seq revealed multiple pacemaker cell-specific accessible regions in the genome of pacemaker-like cells

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

6 Samples

Download data: BED, BIGWIG

(Submitter supplied) We investigated transcriptional profiles of Ptf1a-Cre driven homozygous Tbx3-KO and wildtype pancreata 72h and 168h after onset of acute pancreatitis.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21493

12 Samples

Download data: TSV

(Submitter supplied) To better understand molecular mechanisms of human pancreatic development associated with GATA6 haploinsufficiency, we performed RNA-seq analysis to characterize the biological processes affected by GATA6 heterozygous mutation. We found majority of top downregulated transcription factors are known to play key roles in pancreatic development and top downregulated genes were enriched with factors involved in developmental processes, with the pancreas being the top affected lineage.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: XLS

(Submitter supplied) Here, we developed a new differentiation protocol by mimicking the two-stage development of hepatoblasts to potentiate their transition to hepatic progenitor cells (hiHPCs), which permits the high-efficiency generation of hiHPCs from chemically induced pluripotent stem cells (hCiPSCs). Moreover, hCiPSC-derived hiHPCs can further differentiate into mature hepatocytes (hiHEPs). We use single-cell RNA sequencing (scRNA-seq) to analyze the two-stage of hepatoblasts indicating the similarity between hepatoblasts differentiated in vitro and in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

16 Samples

Download data: MTX, TSV, TXT

(Submitter supplied) Tissues and cells derived from pluripotent stem cells (PSC) are likely to become widely used in disease modeling, drug screening, and regenerative medicine. For these applications, the in vitro PSC differentiation process must be elaborately investigated and controlled to reliably obtain the desired end products. However, because traditional experimental methods, such as one factor at a time (OFAT) or brute-force approaches, are impractical for detailed screening of complex PSC cultivation conditions, more strategic and effective screening based on statistical design of experiments (DOE) ought to be indispensable. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17303

28 Samples

Download data: TXT

(Submitter supplied) Pancreatic beta cell generation from induced pluripotent stem cells (iPSCs) offers an alternative donor tissue source; however, the efficiency of induction of INSULIN (INS)+ cells from human iPSCs (hiPSCs) is low. We aimed to establish an efficient differentiation protocol for generating INS+ cells from hiPSCs by identifying novel inducers. We screened small molecules that increased the induction rate of INS+ cells from hiPSC-derived PDX1+ pancreatic progenitor cells by using high-throughput screening (HTS) system. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TSV

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

Organism:

Mus musculus

Type:

Expression profiling by array

Platforms:

GPL11202 GPL24228 GPL10333

6 Samples

Download data: TXT

(Submitter supplied) Evaluation of the transcriptional changes in E14.5 ureters upon combined loss of Tbx2 and Tbx3 in the ureteric mesenchyme.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL24228

2 Samples

Download data: TXT

(Submitter supplied) Evaluation of the transcriptional changes in E18.5 ureters upon combined loss of Tbx2 and Tbx3 in the ureteric mesenchyme.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL10333

2 Samples

Download data: TXT

(Submitter supplied) Evaluation of the transcriptional changes in E13.5 ureters upon overexpression of Tbx2 in the ureteric mesenchyme.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

2 Samples

Download data: TXT