GEO DataSets

(Submitter supplied) In this study, we used miRNA sequencing to analyze and identify possible miRNAs that can be regulated by and ELF3-AS1 in gastric cancer. The results showed that lncRNA ELF3-AS1 knockdown decreased the expression of miR-33a/b and miR-203a. Due to miR-33a/b and miR-203a were able to target SNAI2 expression, and ELF3-AS1 knockdown significantly upregulates SNAI2 expression, we speculated ELF3-AS1 may negatively regulate SNAI2 expression through positively regulating the expression of miR-33a/b and miR-203a in GC.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23227

3 Samples

Download data: TXT

(Submitter supplied) The oncogene SNAI2 is known to be a master transcription factor that regulates a broad range of cellular processes, including epithelial-mesenchymal transition (EMT). As a transcription factor, there is no doubt that SNAI1/2 could directly regulate the expression of thousands of genes, including lncRNAs. In this study, we took SNAI1/2 as a breakthrough point to screen and identify lncRNAs regulated by SNAI2 in GC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

3 Samples

Download data: TXT

(Submitter supplied) Our data showed that lncRNA ELF3-AS1 could bind on the exon1 of ELF3-201 to form a double-stranded RNA molecule. This double-stranded RNA could interact with ILF2/ILF3 complex. To explore the biofunction of the interaction between ELF3-AS1 and ILF2/ILF3 complex, loss-of-function studies regarding ILF2 and ILF3 were performed in SGC7901 cell line. RNA sequencing studies showed that knockdown of ILF3 significantly decreased ELF3-AS1, while knockdown of ILF2 significantly increased ELF3-AS1 and NF90 expression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) Our data showed that ELF3-AS1 was a nuclear lncRNA, and its biofunction in cancers is largely unknown to date. To explore the function of lncRNA ELF3-AS1 in gastric cancer, loss-of-function study was performed in SGC7901 and AGS cell lines. RNA sequencing studies showed that the expression of almost all the histone coding genes were significantly increased after knocking down of ELF3-AS1 in SGC7901 and AGS cell lines.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23227

8 Samples

Download data: TXT

(Submitter supplied) RNA pulldown assay showed that lncRNA UBE2CP3 could bind to ILF3 protein. In order to further verify the interaction between ILF3 and UBE2CP3, RNA Immunoprecipitation (RIP) assay was performed to identify the RNAs that binds to ILF3 protein. RIP-seq data verifies the interaction between ILF3 and UBE2CP3. Interestingly, UBE2CP3 could also binds to 3'UTR of IGFBP7 mRNA. Mechanismly, lncRNA UBE2CP3 and 3' UTR of IGFBP7 could forms an double-stranded RNA. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL20301

2 Samples

Download data: TXT

(Submitter supplied) In this study, we used miRNA sequencing to analyze and identify possible miRNAs that can be regulated by and UBE2CP3 in gastric cancer. The results showed that lncRNA UBE2CP3 overexpression decreased the expression of miR-138-5p. Due to miR-138-5p was able to target ITGA2 expression, and UBE2CP3 knockdown significantly downregulates ITGA2 expression, we speculated UBE2CP3 may positively regulate ITGA2 expression through sponging miR-138-5p in GC.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23227

4 Samples

Download data: TXT

(Submitter supplied) Our data showed that UBE2CP3 was aberrantly upregulated in gastric cancer (GC), but its biofunction in GC is largely unknown to date. To explore the function of lncRNA UBE2CP3 in gastric cancer, loss-of-function and RNA sequencing studies were performed in SGC7901 cell line. The results showed that depletion of UBE2CP3 significantly decreased the expression of ITGA2. Interestingly, ITGA2 was also a target gene of miR-138. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

9 Samples

Download data: TXT

(Submitter supplied) As one of the most abundant lncRNAs in cells, the biological function of lncRNA FGD5-AS1 remains largely unclear in cancers, especially in gastric cancer (GC). In addition, the reason for such high levels of FGD5-AS1 in cells remains unknown. In this study, FGD5-AS1 was proved to be a ZEB1-related lncRNA which was overexpressed and predicted poor prognosis in GC. Knockdown of FGD5-AS1 decreased GC proliferation in vitro and in vivo. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: XLSX

(Submitter supplied) To reveal PTBP1-bound RNAs, we conducted RNA immunoprecipitation sequencing (RIP-seq) with total RNA samples from MKN-28 cells.

Organism:

Homo sapiens

Type:

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

Platform:

GPL20301

2 Samples

Download data: XLSX

(Submitter supplied) We analysed the transcriptome profile by RNA-seq in PTBP1 knockout and control MKN-28 cells.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

2 Samples

Download data: TXT

(Submitter supplied) We implemented lncRNA microarray analysis in 5 paired gastric cancer tissues and adjacent noncancerous tissues to identify differential expression of lncRNAs and mRNAs in gastric cancer.

Organism:

Homo sapiens

Type:

Expression profiling by array; Non-coding RNA profiling by array

Platform:

GPL20115

5 Samples

Download data: TXT

(Submitter supplied) HOXD9 is a transcription factor reported to facilitate metastasis in gastric cancer. In our study, we tried to figure out the role HOXD9 played in gastric cancer metastasis by obtaining its expression profiling.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: XLSX

(Submitter supplied) Our data showed that NR2F1-AS1 functions oncogenic roles in gastric cancer (GC), but the underlying molecular mechanism remains largely unknown to date. To explore the function of lncRNA NR2F1-AS1 in gastric cancer, loss-of-function and RNA sequencing studies were performed in SGC7901 cell line. The results showed that depletion of NR2F1-AS1 significantly decreased the expression of VAMP7. Interestingly, VAMP7 was also a target gene of miR-29a-3p. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: TXT

(Submitter supplied) Purpose: The goal of the study is to compare NGS-derived transcriptome in an isogenic breast cancer progression model cell line system. By comparing the protein-coding and noncoding gene expression of normal versus tumorigenic breast cancer cell lines, we will be able to identify genes that show aberrant expression during breast cancer progression. Methods: We isolated poly A + RNA from four isogenic mammary epithelial cell lines showing various stages of breast cancer progression. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

8 Samples

Download data: TXT

(Submitter supplied) To explore whether DANCR plays a role in nasopharyngeal carcinoma tumorigenesis, a RNA-seq analysis was performed to compare the gene expression profiles of DANCR siRNA and control groups.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20795

6 Samples

Download data: TXT

(Submitter supplied) HLA-C arose during evolution of pregnancy in the Great Apes 10-15 million years ago. It has a dual function on placental extravillous trophoblasts (EVT) as it contributes to both tolerance and immunity at the maternal-fetal interface. The mode of its regulation is of considerable interest in connection with the biology of pregnancy and pregnancy abnormalities. First trimester primary EVT in which HLA-C is highly expressed, as well as JEG3, an EVT model cell lines, were employed. Single cell RNA-seq data and quantitative PCR identified high expression of the transcription factor ELF3 in those cells. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

5 Samples

Download data: BW

(Submitter supplied) While years of investigation have elucidated many aspects of embryonic stem cell (ESC) regulation, the contributions of post-transcriptional and translational mechanisms to the pluripotency network remain largely unexplored. In particular, little is known in ESCs about the function of RNA binding proteins (RBPs), the protein agents of post-transcriptional regulation. We performed an unbiased RNAi screen of RBPs in an ESC differentiation assay and identified two related genes, NF45 (Ilf2) and NF90/NF110 (Ilf3), whose knockdown promoted differentiation to an epiblast-like state. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL17021

22 Samples

Download data: XLSX

(Submitter supplied) Purpose: Tumor metastasis is the main cause of death from breast cancer patients and cell migration plays a critical role in metastasis. Recent studies have shown long non-coding RNAs (lncRNAs) play an essential role in the initiation and progression of cancer. In the present study, the role of a LncRNA, Rho GTPase Activating Protein 5- Antisense 1 (ARHGAP5-AS1) in breast cancer was investigated. Methods: RNA sequencing was performed to find out dysregulated LncRNAs in MDA-MB-231-LM2 cells. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

4 Samples

Download data: TXT

(Submitter supplied) We profiled esophageal adenocarcinoma cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematically modeling was performed to establish (super)-enhancers landscapes and inter-connected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs was investigated by ChIP-Seq, RNA-Seq, 4C-Seq and luciferase assay. Biological functions of candidate factors were evaluated by measuring cell proliferation, colony formation, cell apoptosis and xenograft growth. more...

Organism:

Homo sapiens

Type:

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

Platform:

GPL10999

6 Samples

Download data: BW, NARROWPEAK, TXT

(Submitter supplied) We performed paired-end poly A+ RNA sequencing using total RNA isolated from serum-starved and serum-released (6-hour) control and MIR222HG-depleted WI-38 cells

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

12 Samples

Download data: TXT