GEO DataSets

(Submitter supplied) Hepatic stellate cells (HSCs) are pericytes of the liver and are responsible for liver fibrosis and cirrhosis, which are end stages of chronic liver diseases. TFG-β activates HSCs leading to differentiation of myofibroblasts in the process of liver fibrosis. While heterogeneity of HSCs is appreciated in the fibrotic liver, it remains elusive which HSC subsets mainly contribute to fibrosis. We here show that expression of pericyte marker, Foxd1, specifically marked a subset of HSCs in the Foxd1-fate tracer mice. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

12 Samples

Download data: TXT

(Submitter supplied) In the developing neocortex, diverse neurons of defined types and numbers are orderly produced by a limited population of radial glial progenitors (RGPs) as they progress through successive cell fate changes. How this temporal patterning is regulated at the molecular level remains largely unknown. Here we describe a high-sensitive single-cell multi-omics assay enabling deep characterization of regulatory programs and an analytical framework integrating joint dynamics in single-cell transcription and chromatin structure with regulation of temporal identities and fate progression of RGPs. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL21273

1634 Samples

Download data: TXT

(Submitter supplied) We used Sequence-Scope (Seq-Scope), which can generate ultra-high definition images of sequence-based molecular signatures resolved at a submicrometer scale, for profiling spatial transcriptome associated with abdominal aortic aneurysm Experimental Methods: Seq-Scope experiment is divided into two consecutive sequencing steps: 1st-Seq and 2nd-Seq. 1st-Seq of Seq-Scope starts with the solid-phase amplification of a single-stranded synthetic oligonucleotide library using an Illumina sequencing-by-synthesis (SBS) platform. more...

Organism:

synthetic construct; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19604 GPL21273

3 Samples

Download data: MTX, TSV

(Submitter supplied) N6-methyladenosine (m6A) is a prevalent modification of mammalian mRNA. Increasing evidence has documented diverse roles of m6A in normal cell physiology and diseases. However, our knowledge on the role of the m6A in erythropoiesis is very limited. A previous study implicated the role of METTL3, the catalytic enzyme for m6A modification, in human erythropoiesis in vitro. But the function role of METTL3 in vivo has yet to investigated. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platforms:

GPL21273 GPL24247

16 Samples

Download data: TXT

(Submitter supplied) We observed that the deletion of Anp32b led to severe defects in ocular development, such as anophthalmia and microphthalmia. Moreover, Anp32b was highly expressed in the lens, and Anp32b−/− embryos with microphthalmia typically exhibited severely impaired lens development. Mechanistically, ANP32B directly interacted with paired box protein 6 (PAX6), a master transcriptional regulator of ocular development, and enhanced its transcriptional activity. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: TXT

(Submitter supplied) Cohesin stalling at CTCF binding sites represents one of the main principles of interphase chromosome organization. In the current studies, we dissect the role of cohesin and CTCF, both alone and in combination, in 3D genome organization by depleting these proteins using acute protein degradation techniques. By systematic examination of interactomic, epigenomic and transcriptomic changes using various sequencing techniques, our studies reveal the functions of cohesin and CTCF in mediating the formation of chromatin loops, topologically associating domains, chromosome compartments and nuclear lamina associating domains. more...

Organism:

Mus musculus

Type:

Other

Platform:

GPL21273

12 Samples

Download data: MCOOL

(Submitter supplied) This study investigates the role of kidney-resident macrophages (KRMs) in modulating susceptibility to tubulointerstitial nephritis (TIN) by selectively depleting KRMs and examining the resulting immunological and pathological changes in the kidney using single-cell RNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

2 Samples

Download data: H5

(Submitter supplied) This study investigates the role of kidney-resident macrophages (KRMs) in modulating susceptibility to tubulointerstitial nephritis (TIN) by selectively depleting KRMs and examining the resulting immunological and pathological changes in the kidney using single-cell RNA sequencing.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

2 Samples

Download data: H5

(Submitter supplied) The purpose of this study is to investigate the long-term depletion of kidney-resident macrophages (KRMs) and their role in regulating tubulointerstitial nephritis (TIN) through specialized efferocytosis and interaction with neighboring T cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

3 Samples

Download data: H5

(Submitter supplied) This study aims to delineate the effects of AXL deletion on kidney development and cellular heterogeneity by analyzing single-cell RNA transcriptomic datasets from 11-week-old male Axl wild type (WT) and heterozygous (het) knockout mice.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

2 Samples

Download data: H5

(Submitter supplied) The three-dimensional (3D) genome structure is essential for gene regulation and various genomic functions. CTCF plays a key role in organizing Topologically Associated Domains (TADs) and promoter-enhancer loops, contributing to proper cell differentiation and development. Although CTCF binds the genome with high sequence specificity, its binding sites are dynamically regulated during development, and aberrant CTCF binding is linked to diseases such as cancer and neurological disorders, and aging. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

11 Samples

Download data: BW

(Submitter supplied) Spry1 cKO mice were found spontaneously developed psoriasis-like skin inflammation and arthritis.To further investigate the periarticular immune microenvironment in paws, single-cell RNA sequencing of the periarticular tissue from Spry1 cKO and control mice was performed.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

6 Samples

Download data: MTX, TSV

(Submitter supplied) In the mammalian neocortex, excitatory neurons that send projections via the corpus callosum are critical to integrating information across the two brain hemispheres. The molecular mechanisms governing the development of the dendritic arbours and spines of these callosal neurons are poorly understood, yet these features are critical to their physiological properties. LIM Homeodomain 2 (Lhx2), a regulator of fundamental processes in cortical development, is expressed in postmitotic callosal neurons occupying layer II/III of the neocortex and also in their progenitors in the embryonic day (E) 15.5 ventricular zone of the mouse neocortex. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

14 Samples

Download data: CSV, TXT

(Submitter supplied) Mammalian embryogenesis involves intricate epigenetic reprogramming and chromatin remodeling. In this study, we investigated the role of Brg1, a catalytic ATPase subunit of the SWI/SNF complex, in early embryonic development and mouse embryonic stem cell (mESC) pluripotency. By generating Smarca4 flox/flox Gdf9-Cre female mice to knockout Brg1 in MII oocytes and using CRISPR-Cas9 to knockout Brg1 in mESCs, we found that Brg1 deficiency led to multiple defects. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

16 Samples

Download data: TAB

(Submitter supplied) The mammalian kidney contains numerous nephrons connected to the collecting ducts, and each nephron consists of a glomerulus, a proximal tubule, the loop of Henle (LoH), and a distal tubule. Folliculin (Flcn) is a causative gene for Birt-Hogg-Dube (BHD) syndrome, which is characterized by a variety of symptoms including renal cysts and cancers. Although deletion of Flcn in the mouse collecting duct has been reported to result in cyst formation, its precise role in the nephron remains unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

2 Samples

Download data: MTX, TSV

(Submitter supplied) In the developing neocortex, a diverse array of neurons with defined types and abundances are systematically generated by a limited population of radial glial progenitors (RGPs) as they undergo successive fate changes. How this temporal patterning is regulated at the molecular level remains largely unknown. Here we present an in-depth single-cell multi-omics assay for deep characterization of regulatory programs, along with an analytical framework that integrates joint dynamics in single-cell transcription and chromatin structure to interrogate the regulation of temporal identities and fate progression of RGPs. more...

Organism:

Mus musculus

Type:

Other; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL21273

26 Samples

Download data: BW, TXT

(Submitter supplied) Glioblastoma (GBM) is the most common and aggressive brain cancer, showing minimal response to available therapies. A highly immunosuppressive tumor microenvironment (TME) contributes to the limited therapeutic response of GBM. Astrocytes are major components of the central nervous system (CNS), with important immunoregulatory roles. However, little is known about the role of astrocytes and their subsets in the immune response to GBM. more...

Organism:

Homo sapiens; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21273 GPL24247 GPL20795

102 Samples

Download data: H5, TAR

(Submitter supplied) Spontaneous cellular reprogramming is rare, but has been observed in adult cells. This is most evident in the mammalian liver, where hepatocytes undergo physiological reprogramming to generate functional biliary epithelial cells (BECs) in response to injury. The underlying mechanisms driving this cell fate switch remain unclear, however. Here, we characterize epigenetic changes occurring during this transition at the single cell level, and show that reprogramming occurs synchronously and deterministically, though reprogrammed cells retain epigenetic hepatocyte memory. more...

Organism:

Escherichia coli; Mus musculus

Type:

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

Platforms:

GPL28126 GPL21273 GPL21626

86 Samples

Download data: BROADPEAK, BW, TBI, TSV, TXT

(Submitter supplied) Colorectal cancer (CRC) cells infiltrating surrounding tissue commonly undergo partial epithelial-mesenchymal transitions (pEMT) and employ a collective mode of invasion. How these phenotypic traits are regulated and possibly interconnected remains underexplored. Here, we used intestinal organoids with CRC driver mutations as model system to investigate the mechanistic basis of TGF‑β1-induced pEMT and collective invasion. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21273

4 Samples

Download data: H5AD

(Submitter supplied) Metastases cause most cancer deaths and reflect cellular transitions from epithelial to mesenchymal states (EMT) that enable primary tumor escape to seeding and growth at metastatic sites. Rare cancer-driving mutations that disrupt mitochondrial oxidative metabolism (OxPhos) can promote EMT, yet molecular mechanisms that more broadly link metabolism to metastases are uncertain. Analyses of clear cell renal cell carcinoma (RCC) cells identified the hypoxia-induced mitochondrial electron transport inhibitor, NDUFA4L2, as highly enriched in cancer cells with EMT signatures. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL21273

8 Samples

Download data: BW