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The differentially expressed genes in SRSF3 siRNA-treated HCT116 cells

ABSTRACT: 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(S): Homo sapiens

PROVIDER: GSE31876 | GEO | 2013/08/04

SECONDARY ACCESSION(S): PRJNA145233

REPOSITORIES: GEO

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The differentially expressed genes in SRSF3 siRNA-treated HCT116 cells

Project description: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. After treatment of HCT116 cells with SRSF3 (sample 02) or control (sample 01) siRNA, total RNA was extracted using RNeasy Mini Kit (Qiagen, Valencia, CA). The quality of the purified RNA and its applicability for microarray analysis were assessed by the Agilent 2100 Bioanalyzer using a RNA 6000 Nano Labchip kit (Agilent Technologies, Palo Alto, CA, USA). Total RNA (400 ng) was used for amplification, labeling and hybridization to a whole human genome oligoDNA microarray (4x44k; Agilent) according to the manufacture’s instructions.

2013-08-04 | E-GEOD-31876 | biostudies-arrayexpress

PAR-CLIP analysis of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 in human HeLa cells

Project description:Label the cells overexpressed Flag tagged YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 with 4-SU, the RNA bound by YTHDC1 and SRSF proteins can be got by Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation using a TruSeqâ¢ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturerâs protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane. Discovery of the binding motif of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 or SRSF10 in overexpressed Human HeLa cells

2016-02-17 | E-GEOD-71096 | biostudies-arrayexpress

Cardiomyocyte-specific Srsf3 deletion reveals a mitochondrial regulatory role

Project description:Serine-rich splicing factor 3 (SRSF3) was recently reported as being necessary to preserve RNA stability via an mTOR mechanism in a cardiac mouse model in adulthood. Here, we demonstrate the link between Srsf3 and mitochondrial integrity in an embryonic cardiomyocyte-specific Srsf3 conditional knockout (cKO) mouse model. Fifteen-day-old Srsf3 cKO mice showed dramatically reduced (below 50%) survival and reduced the left ventricular systolic performance, and histological analysis of these hearts revealed a significant increase in cardiomyocyte size, confirming the severe remodeling induced by Srsf3 deletion. RNA-seq analysis of the hearts of 5-day-old Srsf3 cKO mice revealed early changes in expression levels and alternative splicing of several transcripts related to mitochondrial integrity and oxidative phosphorylation. Likewise, the levels of several protein complexes of the electron transport chain decreased, and mitochondrial complex I-driven respiration of permeabilized cardiac muscle fibers from the left ventricle was impaired. Furthermore, transmission electron microscopy analysis showed disordered mitochondrial length and cristae structure. Together with its indispensable role in the physiological maintenance of mouse hearts, these results highlight the previously unrecognized function of Srsf3 in regulating the mitochondrial integrity.

2021-06-23 | GSE151168 | GEO

PAR-CLIP analysis of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 in human HeLa cells

Project description:Label the cells overexpressed Flag tagged YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 with 4-SU, the RNA bound by YTHDC1 and SRSF proteins can be got by Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

2016-02-17 | GSE71096 | GEO

HCT116 (CRC): control siRNA vs. ZNF746 siRNA Transfected

Project description:Transcriptional profiling of HCT116 cells compared to untreated control with HCT116 cells transfected with ZNF746 siRNA plasmid. Goal was to determine the effects of ZNF746 gene transfection on CRC progression. Two-condition experiment, HCT116 vs. ZNF746 siRNA.

2019-12-01 | GSE90832 | GEO

RNA-Seq analysis of SRSF3 KO hearts compared to controls and iCLIP analysis of SRSF3 binding profile in neonatal cardiomyocytes

Project description: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.

2019-05-27 | GSE123002 | GEO

Identification of Tra2β-associated mRNAs in HCT116 cells

Project description:Human transformer 2β (Tra2β) is a serine/arginine-rich (SR)-like protein splicing factor and is now implicated to play wide-ranging roles in gene expression as an RNA-binding protein. In this study, we identified a subset of Tra2β-associated mRNAs in HCT116 human colon cancer cells using RNA immunoprecipitation with an anti-Tra2β antibody and microarray analysis.

2014-09-03 | GSE60904 | GEO

Transcriptome analysis on TDP43 and SRSF3 downstream genes and binding RNAs in MDA-MB231 cells by Next Generation Sequencing

Project description: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. RIP-seq was also applied to identify binding RNA against Flag antibodies.

2018-12-31 | GSE98016 | GEO

Analysis of gene expression and splicing after doxycycline-induced knockdown of SRSF3

Project description: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. Total RNAs extracted from A2780/SRSF3si2, a subline of ovarian cancer cell line A2780, treated with or without doxycycline at 0.1ug/ml for three days were analyzed using Affymetrix GeneChip® Human Exon 1.0 ST Array

2015-08-06 | E-GEOD-71745 | biostudies-arrayexpress

Identification of Tra2M-NM-2-associated mRNAs in HCT116 cells

Project description:Human transformer 2M-NM-2 (Tra2M-NM-2) is a serine/arginine-rich (SR)-like protein splicing factor and is now implicated to play wide-ranging roles in gene expression as an RNA-binding protein. In this study, we identified a subset of Tra2M-NM-2-associated mRNAs in HCT116 human colon cancer cells using RNA immunoprecipitation with an anti-Tra2M-NM-2 antibody and microarray analysis. Whole-cell extracts from HCT116 cells were incubated with protein-A Sepharose beads precoated with 3 M-NM-<g anti-Tra2M-NM-2 antibody or control rabbit IgG for 2 h at 4M-BM-0C. RNA in the immunoprecipitation (IP) materials was measured by human whole-genome microarray (Agilent Technology).

2014-09-03 | E-GEOD-60904 | biostudies-arrayexpress

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