GEO DataSets

(Submitter supplied) Purpose: The splicing factor SRSF3 is a member of serine- and arginine-rich proteins, which is frequently upregulated in various types of cancer. The aim of this study is to profile the alternative splicing (AS) events that were regulated by SRSF3 in glioma stem-like cells (GSCs). Methods: Total RNAs isolated from GSC83 and GSC528 cells with SRSF3-konckout (KO) or control (WT) were subjected to paired-end RNA-seq using the Illumina NextSeq 500 system according to the manufacturer's instruction. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: TXT

(Submitter supplied) TDP43 and SRSF3 has been reported to be RNA-binding proteins; however their roles in breast cancer progression has not been examined previously. Here, we performed RNA-seq on MDA-MB231 cells stably expressed sh-control, shTDP43, shSRSF3 or sh-TDP43 and sh-SRSF3 using lentivirus in duplicates. In addition, MDA-MB231 cells with stable expression of flag-TDP43 or flag-SRSF3 were also generated by using lentivirus. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) SRSF3 is overexpressed in human invasive ovarian cancer and its overexpression is required for cancer cell growth and survival. To decipher the mechnisms behind the role of SRSF3 in ovarian cancer, we examined the gene expression and splicing in the ovarian cancer cell line that was engineered to express a doxycycline-induced SRSF3 siRNA, which was able to knockdown SRSF3 expression by 90% and induce apoptosis.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

4 Samples

Download data: CEL, CHP

(Submitter supplied) To examine the effects of SRp20 on genome-wide RNA splicing in tumor cells, we utilized Exonhit SpliceArray to compare genome-wide changes of RNA splicing and transcription in U2OS cells with or without knockdown of SRp20 by RNAi.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL7884

6 Samples

Download data: CEL, TXT, XLS

(Submitter supplied) The objective of our study was to determine whether aberrant alternative splicing could play a role in the malignant phenotype of GBM. Patients with GBM were operated with 5-aminolevulinic fluorescence guided surgery. The fluorescent was used to take biopsies from the tumor center, and from adjacent normal-looking tissue. Three paired normal/GBM samples were analyzed in a HJAY J array. We validated our results with conventional PCR and qRT-PCR in those tumor samples and in ten additional GBMs. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL21251

6 Samples

Download data: CEL

(Submitter supplied) Dysregulation of serine/arginine splicing factors (SRSFs) and thereby the abnormal alternative splicing (AS) has been widely implicated in the development of multiple cancers, but scarcely investigated in nasopharyngeal carcinoma (NPC). Here we examine the expression of 12 classical SRSFs between 87 NPC and 10 control samples, revealing a significant upregulation of SRSF3 and its association with worse prognosis in NPC. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

3 Samples

Download data: TXT

(Submitter supplied) To identify new Glioblastoma multiforme (GBM) therapeutic strategies, we previously performed genome-wide RNAi lethality screens in patient-derived GBM stem-like cells (GSCs) and neural progenitor cells (NPCs) to identify genes required for the self-renewal of GSC isolates, but which are dispensable for NPCs. Here we report the retest of the GSC-lethal gene ZNF131, which encodes a novel vertebrate-specific BTB domain zinc finger transcription factor that is broadly required for GSC viability. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) The goal of this study is to analyse the transcriptome of control hearts vs hearts lacking SRSF3 expression and to analyse binding preferences of SRSF3 in cardiac myocytes.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

8 Samples

Download data: BED, XLSX

(Submitter supplied) RNA seqeuncing was performed to identifiy changes in genes expression and alternative splicing following SRSF3 depletion in pluripotent stem cells.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21626

4 Samples

Download data: CSV, XLSX

(Submitter supplied) Somatic cell reprogramming into pluripotent stem cells (iPSC) through the forced expression of defined factors induces changes in genome architecture reflective of the embryonic stem cell state. However, only a small minority of cells typically transition to pluripotency, which has limited our understanding of what defines cells that successfully reprogram. Here, we characterize the changes that occur across the DNA regulatory landscape during reprogramming by time-course profiling of isolated sub-populations of reprogramming intermediates poised to become iPSC. more...

Organism:

Mus musculus

Type:

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

Platform:

GPL18480

85 Samples

Download data: BED, BIGWIG, TXT, XLSX

(Submitter supplied) Purpose:Next-generation sequencing has revolutionized sytems-level celluar pathway analysis. The goals of this study are to compare the U87 cell xenograft GBM mice (U87 cell line) to TWIST1 knock out U87 cell xenograft GBM mice (TWIST1 knock out U87 cell line) using their transcriptomes

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

23 Samples

Download data: TXT

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

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

20 Samples

Download data

(Submitter supplied) Gene knockdown of NAT12/NAA30 led to decreased proliferation, sphere forming ability and mitochondrial hypoxia tolerance in the GSC T65 culture. Intracranial transplantation of these cells into SCID mice showed that the decreased NAT12/NAA30 expression correlated with the prolonged animal survival and reduced tumor size

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

12 Samples

Download data: TXT

(Submitter supplied) This microarray contains expression data for two GBM tissue samples, four GSC cultures grown as spheres and one NFC culture grown as spheres

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL10558

8 Samples

Download data: TXT

(Submitter supplied) We identified non-POU domain-containing octamer-binding protein (NONO), a Drosophila behavior human splicing (DBHS) protein, among the most upregulated mRNA splicing factors in glioblastoma multiforme (GBM). NONO was associated with poor prognosis in GBM patients, and overexpression of NONO promoted GBM cell proliferation, invasion and tumorigenesis in a GBM orthotopic xenograft model. Through RNA sequencing based transcriptomic profiling, we found that knockdown of NONO resulted in global changes in alternative splicing-intron retention, and identified GPX1 and CCN1 as two pre-mRNAs targeted by NONO. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) We identified non-POU domain-containing octamer-binding protein (NONO), a Drosophila behavior human splicing (DBHS) protein, among the most upregulated mRNA splicing factors in glioblastoma multiforme (GBM). NONO was associated with poor prognosis in GBM patients, and overexpression of NONO promoted GBM cell proliferation, invasion and tumorigenesis in a GBM orthotopic xenograft model. Through RNA sequencing based transcriptomic profiling, we found that knockdown of NONO resulted in global changes in alternative splicing-intron retention, and identified GPX1 and CCN1 as two pre-mRNAs targeted by NONO. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

6 Samples

Download data: TXT

(Submitter supplied) Several members of SRSF family play wide-ranging roles in the regulation of transcription and post-splicing processes as well as splice sites selection. Although the expression of SRSF3 was reported to be overexpressed in several cancers, the roles of SRSF3 in the cancer cells are almost unknown. We analyzed differentially expressed genes in SRSF3 siRNA-treated HCT116 cells and identified the specific pathways regulated by SRSF3.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6480

2 Samples

Download data: TXT

(Submitter supplied) Screening small molecules and drugs for activity to modulate alternative splicing, we found that amiloride, distinct from four other intracellular pH-affecting analogues, could “normalize” the splicing of BCL-X, HIPK3 and RON/MISTR1 transcripts in human hepatocellular carcinoma Huh-7 cells. To elucidate the underlying mechanisms, our proteomic analyses of amiloride-treated cells detected hypo-phosphorylation of splicing factor SF2/ASF and also decreased levels of SRp20 and two un-identified SR proteins. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL5188

6 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL16417 GPL24247

9 Samples

Download data: BW

(Submitter supplied) C2C12 cells were UV-irradiated at 400 mJ, and whole cell lysates were harvested from the cells. tRIP was performed as previously described (Masuda et al). Samples were sequenced on the Illumina NovaSeq6000 with 150 bp paired-end read (Macrogen, Japan) or Miseq with 150 bp single-read at the core facility of the Nagoya University. For paired-end read data, only P5 reads were used for analysis. Briefly, after standard HiSeq demultiplexing, reads were adapter-trimmed and reads less than 18 bp were discarded using cutadapt (v1.10). more...

Organism:

Mus musculus

Type:

Other

Platforms:

GPL24247 GPL16417

5 Samples

Download data: BW