GEO DataSets

(Submitter supplied) Scaffold protein IQGAP3 mediates assembly of multiprotein complexes, orchestrating intracellular signaling pathways. Earlier we have found it to be overexpressed in lesional psoriatic skin. IQGAP3 is involved in cell proliferation and chemokine signaling that are key processes in psoriasis, so we decided to investigate the molecular basis of its role in psoriatic phenotype of keratinocytes. Transcriptome profiling of HaCaT keratinocytes allowed us to identify a wide range of psoriasis-associated pathways to be altered in IQGAP3-knockdown cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: XLSX

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

Organism:

Homo sapiens

Type:

Other; Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

23 Samples

Download data

(Submitter supplied) Translation of localized mRNAs serves to regulate specific sites of protein synthesis and its functional activity, whereas translationally inhibited and untranslated mRNAs are compartmentalized for degradation or storage, with no recognized functional role. Here, however, we unexpectedly discover a group of functional, untranslated mRNA sequences that localize to integrin focal adhesions (FAs), dynamic multiprotein assemblies that govern cell movement. more...

Organism:

Homo sapiens

Type:

Other

Platforms:

GPL24676 GPL16791

8 Samples

Download data: CSV

(Submitter supplied) Translation of localized mRNAs serves to regulate specific sites of protein synthesis and its functional activity, whereas translationally inhibited and untranslated mRNAs are compartmentalized for degradation or storage, with no recognized functional role. Here, however, we unexpectedly discover a group of functional, untranslated mRNA sequences that localize to integrin focal adhesions (FAs), dynamic multiprotein assemblies that govern cell movement. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

15 Samples

Download data: CSV

(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 GPL24676

9 Samples

Download data: BIGWIG, WIG

(Submitter supplied) Transcription factors (TFs) engage in various cellular essential processes including differentiation, growth and migration. However, the master TF involved in distant metastasis of nasopharyngeal carcinoma (NPC) remains largely unclear. Here we show that KLF5 regulates actin remodeling to enhance NPC metastasis. We analyzed the msVIPER algorithm-generated transcriptional regulatory networks and identified KLF5 as a master TF of metastatic NPC linked to poor clinical outcomes. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24676 GPL16791

6 Samples

Download data: BIGWIG, WIG

(Submitter supplied) We have used our protocol for generating cortical interneurons from human embryonic stem cells (hESCs) to study gene expression changes during this process, to identify regulatory networks critical to cortical interneuron development. Samples were collected at day 0 (hESCs), day 15 (ventral telencephalic patterned medial ganglionic eminence-like progenitors), day 35 (immature interneurons), and day 60 (mature interneurons).

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

15 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:

GPL24676 GPL16791

118 Samples

Download data: BIGWIG, BROADPEAK, NARROWPEAK

(Submitter supplied) Background Nucleosome repositioning in cancer is believed to cause many changes in genome organisation and gene expression. Understanding these changes is important to elucidate fundamental aspects of cancer. It is also important for medical diagnostics based on cell-free DNA (cfDNA), which originates from genomic DNA regions protected from digestion by nucleosomes. Results We have generated high-resolution nucleosome maps in paired tumour and normal tissues from the same breast cancer patients using MNase-assisted histone H3 ChIP-seq and compared them with the corresponding cfDNA from blood plasma. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL24676

17 Samples

Download data: BED, BW

(Submitter supplied) Transcriptomic comparison of stages of clonal evolution of Fanconi anemia modeled using induced pluripotent stem cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 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; Other

Platforms:

GPL16791 GPL30173

117 Samples

Download data

(Submitter supplied) Background: CD4+CD25hiCD127lo/-FOXP3+ regulatory T cells (Tregs) play a key role in preventing autoimmunity. In type 1 diabetes, adoptive transfer of autologous polyclonal Tregs has been shown to be safe in adults in Phase I clinical trials. Methods: We explore factors contributing to efficacy in autologous polyclonal expanded Tregs (expTregs) Phase 2 clinical trial in 111 children and adolescents with new-onset type 1 diabetes (Sanford/Lisata Therapeutics Trex Phase 2 clinical trial) randomized 1:1:1 high and low treatment to placebo. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

105 Samples

Download data: CSV

(Submitter supplied) T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive immature T-cell cancer. Hotspot mutations in JAK-STAT pathway members IL7R, JAK1 and JAK3 were analyzed in depth, but the role of STAT5A or STAT5B in T-cell development or T-ALL transformation is unclear. Importantly, the driver mutation STAT5BN642H encodes the most frequent activating STAT5 variant in T-ALL and it correlated with disease relapse upon chemotherapy. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: BW, NARROWPEAK

(Submitter supplied) Global m6A-modified mRNAs in undecidualized and decidualized primary human endometrial stromal cells were analyzed by using methylated RNA immunoprecipitation sequencing (MeRIP-seq)

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

4 Samples

Download data: NARROWPEAK

(Submitter supplied) We developed an in vitro model in which primary human endometrial stromal cells (HESCs) were induced to differentiate through treatment with MPA and 8-Br-cAMP. SiRNA-mediated knockdown of METTL3 was performed on HESCs, 6 h prior to treatment of 8-Br-cAMP and MPA.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

4 Samples

Download data: TXT

(Submitter supplied) Pleural fibrosis is defined as an excessive deposition of extracellular matrix (ECM) that results in destruction of the normal pleural tissue architecture and compromised function. However there is currently no effective medication for pleural fibrosis. Understanding the detailed mechanisms of pleural fibrosis is an important unmet need which could lead to the identification of new targets for treatment of this condition. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

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

30 Samples

Download data: BEDGRAPH

(Submitter supplied) Genome wide localization of SUMO1 and SUMO2/3 proteins revealed an asscociation of SUMO proetins with active chromatin. SUMO proteins are enriched at super enhancers and enhancers and SUMOylation regulates a subset of these super enhancers. Super enhancers regulated by SUMOylation were enriched for transcription factor TFAP2C and SUMOylation negatively regulates TFAP2C localization to enhancers and super enhancers. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

22 Samples

Download data: BEDGRAPH

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

6 Samples

Download data: TXT

(Submitter supplied) Ribosome profiling (Ribo-seq) analysis to identify number of ribosome-protected reads from CBC-associated mRNAs or eIF4E-associated mRNAs encoding either a signal sequence or transmembrane domain (TMD)

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

4 Samples

Download data: TXT