GEO DataSets

(Submitter supplied) Type I low-grade gliomas (LGGs), characterized by 1p/19q co-deletions and IDH1/2 mutations, show superior overall survival compared to other gliomas. Approximately 70% of cases harbour mutations in the Capicua (CIC) gene, whose product is a transcriptional repressor whose transcriptional network has yet to be extensively studied in human cells. To address this, we developed CIC knockout cell lines and used transcriptome analyses to study the consequences of CIC loss. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

6 Samples

Download data: CEL

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL20795

116 Samples

Download data: BED, NARROWPEAK, TSV

(Submitter supplied) Capicua (CIC)’s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC’s role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co-occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. more...

Organism:

Homo sapiens

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL20795

12 Samples

Download data: BED

(Submitter supplied) Capicua (CIC)’s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC’s role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co-occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

18 Samples

Download data: TSV

(Submitter supplied) Capicua (CIC)’s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC’s role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co-occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

2 Samples

Download data: NARROWPEAK

(Submitter supplied) Capicua (CIC)’s transcriptional repressor function is implicated in neurodevelopment and in oligodendroglioma (ODG) aetiology. However, CIC’s role in these contexts remains obscure, primarily from our currently limited knowledge regarding its biological functions. Moreover, CIC mutations in ODG invariably co-occur with a neomorphic IDH1/2 mutation, yet the functional relationship between these two genetic events is unknown. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

84 Samples

Download data: BED

(Submitter supplied) Aberrations in Capicua (CIC) have recently been implicated as a negative prognostic factor in a multitude of cancer types through activation of the MAPK signalling cascade and derepression of oncogenic ETS transcription factors. The Ataxin-family protein ATXN1L has previously been reported to interact with CIC in developmental and disease contexts to facilitate the repression of CIC target genes. To further investigate this relationship, we performed functional in vitro studies utilizing ATXN1LKO and CICKO human cell lines and characterized a reciprocal functional relationship between CIC and ATXN1L.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

15 Samples

Download data: TXT

(Submitter supplied) Mutations affecting the RAS-MAPK pathway frequently occur in relapse neuroblastoma tumors, which suggests that activation of this pathway is associated with a more aggressive phenotype. To explore this hypothesis we generated several model systems to define a neuroblastoma RAS-MAPK pathway signature. We could show that activation of this pathway in primary tumors indeed correlates with poor survival and is associated with known activating mutations in ALK and other RAS-MAPK pathway genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

18 Samples

Download data: CEL

(Submitter supplied) CIC encodes a transcriptional repressor and MAPK signalling effector that is inactivated by loss-of-function mutations in several cancer types, consistent with a role as a tumour suppressor. Here, we used bioinformatic, genomic, and proteomic approaches to investigate CIC’s interaction networks. We observed both previously identified and novel candidate interactions between CIC and SWI/SNF complex members, as well as novel interactions between CIC and cell cycle regulators and RNA processing factors. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

7 Samples

Download data: CSV, MTX, TSV

(Submitter supplied) Mouse neural stem cells were generated from conditional knockout mice (Cicflox/flox) or the wild trype control mice (Cic+/+). Cic is conditionally knocked out following expression of Cre-recombinase. Cre-recombinase was incorporated in vitro via adenoviral-Cre transduction.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL18233

14 Samples

Download data: CEL

(Submitter supplied) RNA sequencing of T-ALL tumors derived from genetically modified mouse models: CIC loss-of-function, HRASG12V driven from the Kras promoter and Trp53 KO. Results provide insight into the role of the RAS/CIC axis in T-ALL development.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

15 Samples

Download data: XLS

(Submitter supplied) We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of MAPK genes in various tissues or organs. Cucumber plants of the ‘Jinyan No.4’ cultivar were reared in growth chambers at 28 ± 1 °C with a photoperiod of 16 h light/8 h dark and light intensity of 400 μmol m−2 s−1. The roots, leaves, stems, female flower buds (approximately 3 d before anthesis), male flower buds (approximately 1.0 cm in length), and fruits (10 d after pollination) were collected from flowering plants for tissue expression analysis.

Organism:

Cucumis sativus

Type:

Expression profiling by RT-PCR

Platform:

GPL20125

6 Samples

Download data: TXT

(Submitter supplied) We used Bio-Rad laboratories, lnc. PCR assay panel to analyze expression levels of MAPK genes under various stress conditions and plant hormone treatments. Cucumber plants of the ‘Jinyan No.4’ cultivar were reared in growth chambers at 28 ± 1 °C with a photoperiod of 16 h light/8 h dark and light intensity of 400 μmol m−2 s−1. Three-week-old seedlings were used for all abiotic and biotic treatments. more...

Organism:

Cucumis sativus

Type:

Expression profiling by RT-PCR

Platform:

GPL20125

28 Samples

Download data: TXT

(Submitter supplied) We performed a genome-scale CRISPR screen in a KRAS-mutant pancreatic cancer cell line treated with the MEK inhibitor trametinib, and found that loss of the transcriptional repressor CIC confers resistance to MEK inhibition. We determined that CIC loss also confers resistance to MEK or BRAF inhibition in lung cancer, colorectal cancer, and melanoma cell lines with mutant RAS or BRAF. CIC is a transcriptional repressor that is phosphorylated and inhibited by the MAPK pathway. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

48 Samples

Download data: DIFF

(Submitter supplied) To identify which genes were regulated by CIC in human prostate cancer cell, the effect of CIC knockdown on PC3 cell transcriptome was determined

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10999

4 Samples

Download data: DIFF

(Submitter supplied) AEBP1 has been identified as a transcriptional repressor playing a significant role in adipogenesis. Recently, we have found that AEBP1 is specifically upregulated in primary glioblastoma. We have used gene silencing to identify genes perturbed upon AEBP1 downregulation and ChIP-chip technique to identify its genomic targets of binding and regulation to understand the un-annotated/undescribed role of this transcription factor in gliomagenesis.

Organism:

Homo sapiens

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL570 GPL4125 GPL4124

13 Samples

Download data: CEL, TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5936

88 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of colonic tumors compared to paired adjacent non-tumoral colonic tissue by two strategies. The first strategy is a conventional microarray assay, while the second strategy involves a previous Suppression Subtractive Hybridization (SSH) followed by a conventional microarray assay. We applied subtractive hybridization followed by microarray analysis to identify tumor-specific low-abundance transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5936

40 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of gastric tumors compared to paired adjacent non-tumoral gastric tissue by two strategies. The first strategy is a conventional microarray assay, while the second strategy involves a previous Suppression Subtractive Hybridization (SSH) followed by a conventional microarray assay. We applied subtractive hybridization followed by microarray analysis to identify tumor-specific low-abundance transcripts. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5936

48 Samples

Download data: GPR

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

Organism:

Rattus norvegicus

Type:

Genome binding/occupancy profiling by high throughput sequencing; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL16312 GPL14844 GPL17155

7 Samples

Download data: BED, PAIR