GEO DataSets

(Submitter supplied) By integrating genome-wide copy number alteration, RNA-seq and proteomics data from 589 colorectal cancer (CRC) patients, we revealed that chromosome 8q24.21 amplification is negatively correlated with p53 protein stability. Using siRNA and CRISPR activation screening, we pinpointed a novel long noncoding gene (PiHL, P53 inHibiting LncRNA) from 8q24.21 as a p53 negative regulator. PiHL is drastically upregulated in CRC and is an independent predictor of CRC poor prognosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

6 Samples

Download data: XLS

(Submitter supplied) Genome-wide association studies of tumor samples have identified a large number of lncRNAs associated with various types of cancer including colorectal cancer. To elucidate the mechanism by which CASC9 regulates colorectal cancer cell growth, RNA-sequencing was performed to analyze the gene expression profile affected by CASC9 knockdown. A total of 249 significantly upregulated genes and 491 significantly downregulated genes (absolute fold change ≥ 2, P < 0.05) were found in CASC9 knockdown HCT-116 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) We performed methylated RNA immunoprecipitation followed by sequencing (MeRIP–seq) combined with transcription sequencing to clarify the mechanism underlined YTHDF3 in CRC

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

8 Samples

Download data: XLSX

(Submitter supplied) Analysis of RNA-seq-based differential expression after overexpression of GAS5 or knockdown of YAP revealed a highly significant overlap of common targets.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) The analysis of the RNA-binding protein immunoprecipitation sequencing (RIP-seq) experiment is performed to identified YAP-specific binding lncRNAs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: XLS

(Submitter supplied) Thousands of long noncoding RNAs (lncRNAs) are aberrantly expressed in various types of cancers, however our understanding of their role in the disease is still very limited. We applied RNAseq analysis from patient-derived data with validation in independent cohort of patients. We followed these studies with gene regulation analysis as well as experimental dissection of the role of the identified lncRNA by multiple in vitro and in vivo methods. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: TXT

(Submitter supplied) Increasing evidence suggested that small nucleolar RNAs (snoRNAs) and long non-coding RNAs (LncRNAs) were master regulators of gene regulation at epigenetic modification level, however, the underlying mechanism in colorectal cancer (CRC) have not been investigated. To demonstrate the involvement of LncRNA and snoRNAs in 2’-O-methylation (Me) in tumorigenesis, we develop the LncRNAs-snoRNAs microarray of paired CRC tissues, and found an unrecognized ZFAS1-NOP58- SNORD12C/78 signaling axis in CRC tumorigenesis through recognizing the consensus AAGA motif of ZFAS1 which directly binds to NOP58 protein, and accelerating the snoRNPs assemble for further guiding 2’-O-Me of 28S rRNA. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

8 Samples

Download data: CEL

(Submitter supplied) To further explore the underlying mechanism of PNO1 knockdown on suppression of CRC cell growth in vivo and in vitro, Affymetrix human GeneChip primeview arrays were performed to determine the global gene expression in HCT116 cells after transduction lentivirus encoding PNO1 shRNA (n=3) or control shRNA (n=3).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL15207

6 Samples

Download data: CEL

(Submitter supplied) The E3 ligase MDM2 promotes tumor growth and progression by inducing ubiquitin-mediated degradation of P53 and other tumor suppressing proteins. Here, we identified an MDM2-interacting lncRNA NRON, which promotes tumor formation by suppressing both P53-dependent and independent pathways. NRON binds to MDM2 and MDMX (MDM4) via two different stem-loops respectively and induces their heterogenous dimerization, thereby enhancing the E3 ligase activity of MDM2 towards its tumor suppressing substrates, including P53, RBI and NFATI, etc.

Organism:

Homo sapiens

Type:

Other

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Enriched p53 signalling after MILIP knockdown was validated by RNA-seq; A c-myc reponsive lncRNA MILIP is commonly upregulated in diverse cancer types. RNA-seq analysis of A549 cells following MILIP knockdown revealed that p53 signalling was the mostly enriched gene pathway, suggesting c-Myc may inactivate p53 through MILIP in cancer.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

2 Samples

Download data: TXT

(Submitter supplied) To elucidate whether Fusobacterium Nucleatum(Fn) plays a role in colorectal cancer tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of Fn treated HCT116 colorectal cancer cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

6 Samples

Download data: TXT

(Submitter supplied) Previous studies have documented that long non-coding RNAs participate in a wide-spectrum of biological processes. We hypothesized that long non-coding RNAs may promote glycolysis and tumorigenesis in colorectal cancer by manipulating of target genes. To test this hypothesis, we performed a global non-coding RNA expression profiling in 10 CRC tissues.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

10 Samples

Download data: TXT

(Submitter supplied) FLANC is significantly up-regulated in two cohorts of CRC samples and high level of FLANC is associated with poor patient survival in two additional independent cohorts. FLANC influences cellular growth, apoptosis, migration and metastases formation of CRC cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10332

2 Samples

Download data: TXT

(Submitter supplied) FLANC is significantly up-regulated in two cohorts of CRC samples and high level of FLANC is associated with poor patient survival in two additional independent cohorts. FLANC influences cellular growth, apoptosis, migration and metastases formation of CRC cells.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL4133

2 Samples

Download data: TXT

(Submitter supplied) In this study, we aimed to explore RNAs profiling regulated by LNPPS in bladder cancer. RNA-seq analysis of three pairs of LNPPS-overexpressing 5637 cells and control cells was completed in this project. A total of 17.6Gb raw data was obtained. In concluion, our data showed that the overexpression of LNPPS caused the significantly upregulation of 82 mRNAs, and the downregulation of 102 mRNAs (|Log2FC|>1.5, p<0.05). more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: XLSX

(Submitter supplied) In this study, we aimed to seek out abnormal noncoding RNAs (lncRNAs and circRNAs) involved in the development of bladder cancer through RNA-seq analysis. Transcriptome analysis of five pairs of bladder cancer tumor tissues and matched adjacent non-tumor tissues was completed in this project. A total of 68.18Gb clean data (sequencing data after quality control) was obtained. In conclusion, high-throughput sequencing analysis provided a distinctive landscape for the expression of noncoding RNAs and screened a series of significantly differently expressed lncRNAs and circRNAs, such as lncRNA LNPPS (ENST00000622374) and circSLC38A1. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20301

10 Samples

Download data: TXT, XLSX

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

Organism:

Homo sapiens

Type:

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

Platforms:

GPL9052 GPL17586 GPL11154

15 Samples

Download data: CEL, TXT, WIG

(Submitter supplied) We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are non coding and are differentially expressed by the DNA damage drug.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are non coding and are differentially expressed by the DNA damage drug.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9052

2 Samples

Download data: WIG

(Submitter supplied) We report the application of high-throughput sequencing to performed the p53 regulated trancriptome in HCT116 colon cancer cells treated with the DNA damage 5FU. To study the direct targets of p53 we performed ChIP-seq to deterrmined the p53 biding sites and associated with the expression levels. With this study we identified the new genomic regions regulated by p53 and with special attention in those regions that are significally expressed by DNA damage and and are non- coding.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL17586

9 Samples

Download data: CEL