GEO DataSets

(Submitter supplied) Single Embryo Repli-Seq was utilized to investigate the replication timing in zygotes and 2-cell cleavage stage embryos. The aim was to understand the temporal progression of DNA replication during the early stages of embryonic development in mammals.

Organism:

Mus musculus

Type:

Other

Platforms:

GPL21626 GPL19057

127 Samples

Download data: BED, BEDGRAPH

(Submitter supplied) Branching morphogenesis is essential for the successful development of a functional lung to accomplish its gas exchange function. Although many studies have highlighted requirements for the bone morphogenetic protein (BMP) signaling pathway during branching morphogenesis, little is known about how BMP signalingis regulated. Here we report that the protein arginine methyltransferase 5 (Prmt5) and symmetric dimethylation at histone H4 arginine 3 (H4R3sme2) directly associate with chromatin of Bmp4 to suppress its transcription. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

5 Samples

Download data: TXT

(Submitter supplied) The diverse T cell receptor (TCR) repertoire – generated randomly through VDJ recombination early in development – is inherently self-reactive. Clonal deletion and diversion to regulatory T cell (Treg) fate are key central tolerance mechanisms engaged during thymic selection. The NR4A family of transcription factors has been implicated in both, but the extent of its contribution to clonal deletion and the transcriptional mechanisms at play remain unknown. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

9 Samples

Download data: TXT

(Submitter supplied) Glycogen storage disease type III (GSDIII) is a rare metabolic disorder due to glycogen debranching enzyme (GDE) deficiency. Reduced GDE activity leads to pathological glycogen accumulation in liver, and in cardiac and skeletal muscles, responsible for impaired hepatic metabolism, heart function impairment, and muscle weakness. To date, there is no curative treatment for GSDIII. The large 4.6 kb coding sequence of GDE represents a major limitation toward the development of clinically relevant AAV gene transfer strategy for GSDIII. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

36 Samples

Download data: XLSX

(Submitter supplied) Somatic mutations in non-malignant tissues are selected for because they confer increased clonal fitness, however, it is uncertain if these clones can benefit organ health. Here, ultra-deep targeted sequencing of 150 liver samples from 30 chronic liver disease patients revealed recurrent somatic mutations. PKD1 mutations were observed in 30% of patients, whereas they were only detected in 1.3% of hepatocellular carcinomas (HCCs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

19 Samples

Download data: CSV

(Submitter supplied) Somatic mutations in non-malignant tissues are selected for because they confer increased clonal fitness, however, it is uncertain if these clones can benefit organ health. Here, ultra-deep targeted sequencing of 150 liver samples from 30 chronic liver disease patients revealed recurrent somatic mutations. PKD1 mutations were observed in 30% of patients, whereas they were only detected in 1.3% of hepatocellular carcinomas (HCCs). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

14 Samples

Download data: TSV

(Submitter supplied) The liver plays a central role in whole body metabolic regulation. Studies of liver metabolism are mostly done in vivo in animal models due to the lack of reliable in vitro systems that can recapitulate liver metabolic functions and their regulation. Hepatocyte organoids (HOs) generated in vitro recently are powerful tools for liver regeneration. Here we developed a novel culture condition that enabled successful generation of mature hepatocyte organoids (MHOs) with metabolic functions characteristic of adult livers. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21626 GPL32159

45 Samples

Download data: TXT

(Submitter supplied) The transcriptional response to hypoxia is temporally regulated yet the molecular underpinnings and physiological implications are unknown. We examined herein the roles of hepatic Bmal1 and Hif1a in the circadian response to hypoxia in mice. We found that the majority of the transcriptional response to hypoxia is dependent on Bmal1 or Hif1a, through shared and distinct roles that are daytime determined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

39 Samples

Download data: XLSX

(Submitter supplied) Neuroinflammation is a recognized complication of immunotherapeutic approaches such as immune checkpoint inhibitor treatment, chimeric antigen receptor therapy, and graft versus host disease (GVHD) occurring after allogeneic hematopoietic stem cell transplantation. While T cells and inflammatory cytokines play a role in this process, the precise interplay between the adaptive and innate arms of the immune system that propagates inflammation in the central nervous system remains incompletely understood. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

4 Samples

Download data: MTX, TSV

(Submitter supplied) Determining protein function in a systematic and comprehensive manner is a key goal in modern molecular biology research but is challenging with current approaches. Here, we introduce ORFtag, a versatile method for the massively parallel protein tagging and interrogation of protein function at the proteome scale with minimal effort and expense. We demonstrate the versatility of ORFtag in mouse and human cells with a series of functional screens for transcriptional activators, repressors and post-transcriptional gene regulatory proteins.

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

4 Samples

Download data: TXT

(Submitter supplied) The comprehensive assessment of protein function is a key aim in modern biology yet has proven difficult with existing approaches. Here, we introduce ORFtag, a versatile tool for the massively parallel protein tagging and functional screening at proteome scale. ORFtag integrates a cassette bearing a promoter, the coding sequence of a protein tag, and a splice-donor site, which allows the tag to be expressed and spliced to genomic protein-coding exons and thus enables endogenous protein tagging at minimal expenditure and effort. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

4 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Determining protein function in a systematic and comprehensive manner is a key goal in modern molecular biology research but is challenging with current approaches. Here, we introduce ORFtag, a versatile method for the massively parallel protein tagging and interrogation of protein function at the proteome scale with minimal effort and expense. We demonstrate the versatility of ORFtag in mouse and human cells with a series of functional screens for transcriptional activators, repressors and post-transcriptional gene regulatory proteins.

Organism:

Mus musculus

Type:

Other

Platforms:

GPL21626 GPL21103

12 Samples

Download data: TXT

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

Organism:

Mus musculus

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL21626 GPL21103 GPL19057

28 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) The transcriptional response to hypoxia is temporally regulated yet the molecular underpinnings and physiological implications are unknown. We examined herein the roles of hepatic Bmal1 and Hif1a in the circadian response to hypoxia in mice. We found that the majority of the transcriptional response to hypoxia is dependent on Bmal1 or Hif1a, through shared and distinct roles that are daytime determined. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

8 Samples

Download data: XLSX

(Submitter supplied) The study of HIV infection and pathogenicity in physical reservoirs requires a biologically relevant model which resembles the human immune system and physiology. The human immune system (HIS) mouse is an established model of HIV infection1–3, but defects in immune tissue reconstitution remain a challenge for examining pathology in tissues1,3–7. Herein we show that exogenous injection of the human cytokine FLT-3L into the hematopoietic stem cell (HSC) cord blood HIS mouse model significantly expanded the total area of axillary lymph nodes and the absolute number of circulating human T cells, thus enabling us to visualize and quantify HIV infectivity in the secondary lymphoid tissues of the spleen and axillary node. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

9 Samples

Download data: TSV

(Submitter supplied) Using ATAC-seq analysis from GNPs to MBSHH we discovered a massive modification in chromatin accessibility during MBSHH formation. Next, using integrative bioinformatics, we identified genes of the nuclear factor I (NFI) family that function as oncogenes on the MBSHH epigenome. We demonstrate not only that these genes are essential in the early stages of murine MBSHHs tumorigenesis, but also that their genetic silencing inhibits tumor growth in murine and human MBSHHs in vitro and in vivo. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21626

6 Samples

Download data: H5, TSV

(Submitter supplied) Using ATAC-seq analysis from GNPs to MBSHH we discovered a massive modification in chromatin accessibility during MBSHH formation. Next, using integrative bioinformatics, we identified genes of the nuclear factor I (NFI) family that function as oncogenes on the MBSHH epigenome. We demonstrate not only that these genes are essential in the early stages of murine MBSHHs tumorigenesis, but also that their genetic silencing inhibits tumor growth in murine and human MBSHHs in vitro and in vivo. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21626

9 Samples

Download data: BED

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

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

54 Samples

Download data: BED, H5, TSV

(Submitter supplied) Using ATAC-seq analysis from GNPs to MBSHH we discovered a massive modification in chromatin accessibility during MBSHH formation. Next, using integrative bioinformatics, we identified genes of the nuclear factor I (NFI) family that function as oncogenes on the MBSHH epigenome. We demonstrate not only that these genes are essential in the early stages of murine MBSHHs tumorigenesis, but also that their genetic silencing inhibits tumor growth in murine and human MBSHHs in vitro and in vivo. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

21 Samples

Download data: BED

(Submitter supplied) Using ATAC-seq analysis from GNPs to MBSHH we discovered a massive modification in chromatin accessibility during MBSHH formation. Next, using integrative bioinformatics, we identified genes of the nuclear factor I (NFI) family that function as oncogenes on the MBSHH epigenome. We demonstrate not only that these genes are essential in the early stages of murine MBSHHs tumorigenesis, but also that their genetic silencing inhibits tumor growth in murine and human MBSHHs in vitro and in vivo. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21626

18 Samples

Download data: BED