GEO DataSets

(Submitter supplied) Purpose: High-throughput RNA sequencing has accelerated discovery of the complex regulatory roles of small RNAs, such those derived from tRNAs. Also recent advances in high-throughput RNA sequencing has revealed the complex RNA modification landscape and the complex role these nucleosides modifactions have in cell signalling, stem cell biology, development and cancer. The goal of this study is to establish how m5C-tRNA methylation and tRNA-derived small RNAs can affect stem cell fucntion in cancer. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9250

16 Samples

Download data: BEDGRAPH

(Submitter supplied) Whether protein synthesis and cellular stress response pathways interact to control stem cell functions is currently unknown. Here, we show that skin stem cells synthesise less protein than their immediate progenitors in vivo, even when forced to proliferate in a tumour model. Our analyses reveal that activation of stress response pathways drives both a global reduction of protein synthesis and altered translation of specific mRNAs that together promote stem cell functions and tumourigenesis. more...

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Other

Platform:

GPL9250

28 Samples

Download data: BEDGRAPH

(Submitter supplied) Purpose: Ribosome profiling has revolutionized systems-based analysis and which produces a “global snapshot” of all the ribosomes translationally active in a cell at a particular moment. The goals of this study are to first apply ribosome profiling to in vivo samples for the first time and in particular to stem cells and tumours and second to determine which mRNAs are being actively translated in these particular situations. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL9250

12 Samples

Download data: BEDGRAPH

(Submitter supplied) Analysis of skin lesions from adult mice with epidermal conditional deletion of heterotrimeric G protein Galpha s in cytokeratin 14 positive cells, compared with control mouse skin. Epidermal Gnas ablation leads to skin defects, including basal cell carcinoma (BCC). Results provide insight into role of Galpha s in the regulation of stem cells from the skin.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL11202

8 Samples

Download data: TXT

(Submitter supplied) Post-transcriptional regulatory mechanisms are crucial for protein synthesis during spermatogenesis and often organized by the chromatoid body. Chromatoid bodies are large cytoplasmic ribonucleoprotein granules, whose precise function and composition remain unclear. Here, we identify NSun2 as a novel component of the chromatoid body, and further show that this RNA methylase is essential for germ cell differentiation in the mouse testis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

24 Samples

Download data: TXT

(Submitter supplied) The Lhx2 transcription factor plays essential roles in morphogenesis and patterning of ectodermal derivatives, as well as in controlling stem cell activity. Lhx2 is expressed in the hair follicle (HF) buds, while in postnatal telogen HFs Lhx2+ cells reside in the stem cell-enriched epithelial compartments (bulge, secondary hair germ) and co-express selected stem cell markers (Sox9, Tcf4 and Lgr5). Lhx2+ cells represent the vast majority of cells in the bulge and secondary hair germ that proliferate in response to skin injury. more...

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9833

1 Sample

Download data: GFF, PAIR

(Submitter supplied) The Lhx2 transcription factor plays essential roles in morphogenesis and patterning of ectodermal derivatives, as well as in controlling stem cell activity. Lhx2 is expressed in the hair follicle (HF) buds, while in postnatal telogen HFs Lhx2+ cells reside in the stem cell-enriched epithelial compartments (bulge, secondary hair germ) and co-express selected stem cell markers (Sox9, Tcf4 and Lgr5). Lhx2+ cells represent the vast majority of cells in the bulge and secondary hair germ that proliferate in response to skin injury. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

1 Sample

Download data: TXT

(Submitter supplied) We report the ATAC-SEQ results of BCSCsSETD4 and BCSCsGFP. To explore epigenetic regulation mechnism in BCSC quiescence, Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) were performed in BCSCsSETD4 and BCSCsGFP. Quiescent BCSCsSETD4 showed marked enrichment of H4K20me3 modifications relative to BCSCsGFP.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: TSV

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: CSV, XLSX

(Submitter supplied) We report the single-cell transcriptome of breast cancer stem cells (BCSCs) from solid tumors taken from NOD/SCID mice.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: CSV, XLSX

(Submitter supplied) We report the single-cell transcriptome of breast cancer stem cells (BCSCs) from MCF7 cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

1 Sample

Download data: CSV, XLSX

(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

Platform:

GPL24676

4 Samples

Download data: TXT

(Submitter supplied) We report the whole transcriptome of BCSCsSETD4 and BCSCsGFP

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: TXT

(Submitter supplied) We report the ChIP-SEQ results of H4K20me3 in BCSCsSETD4 and BCSCsGFP. To explore epigenetic regulation by H4K20me3 in BCSC quiescence, we performed chromatin immunoprecipitation sequencing (ChIP-seq) using BCSCsSETD4 and BCSCsGFP. Quiescent BCSCsSETD4 showed marked enrichment of H4K20me3 modifications relative to BCSCsGFP.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

2 Samples

Download data: TXT

(Submitter supplied) We report the whole transcriptome of BCSCs, qBCSCs, and activated qBCSCs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

9 Samples

Download data: TXT

(Submitter supplied) It is known that Rho GTPases control different aspects of the biology of skin stem cells (SSCs). However, little information is available on the role of its upstream regulators under normal and tumorigenic conditions in this process. To address this issue, we have used here mouse models in which the activity of guanosine nucleotide exchange factors of the Vav subfamily has been manipulated using both gain- and loss-of-function strategies. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6246

20 Samples

Download data: CEL

(Submitter supplied) We used microarrays to assess the global gene expression profiles of cancer stem cells which were isolated from cutaneous squamous cell carcinomas which developed when WT, TGF beta receptor II ko, FAK KO, and TGF beta receptor II/FAK double KO were subjected to continuous DMBA treatment. Squamous cell carcinoma stem cells were compared to epidermal progenitor cells (CD49fhighCD34low) and hair follicle bulge stem cells (CD49fhighCD34high).

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

20 Samples

Download data: CEL

(Submitter supplied) Cancer stem cells (CSCs) have been reported in various cancers including skin squamous cell carcinoma (SCC). The molecular mechanisms regulating tumour initiation and stemness are still poorly characterized. Here, we found that Sox2, a transcription factor expressed in various types of embryonic and adult stem cells (SCs), was the most upregulated transcription factor in CSCs of squamous skin tumours. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

6 Samples

Download data: CEL

(Submitter supplied) Cancer stem cells (CSCs) have been reported in various cancers including skin squamous cell carcinoma (SCC). The molecular mechanisms regulating tumour initiation and stemness are still poorly characterized. Here, we found that Sox2, a transcription factor expressed in various types of embryonic and adult stem cells (SCs), was the most upregulated transcription factor in CSCs of squamous skin tumours. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

4 Samples

Download data: CEL

(Submitter supplied) Hippo signalling has been implicated as a key regulator of tissue regeneration. In the intestine, ex vivo organoid cultures model aspects of crypt epithelial regeneration. Therefore in order to uncover the Yap regulated transcriptional programs during crypt regeneration we performed RNA-sequencing of Yap wt and Yap deficient organoids, as well as organoids inducibly expressing Yap.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

4 Samples

Download data: TXT