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Genome-wide map of Six4 in C2C12 cells 24 hours post-differentiation

ABSTRACT: In this study, we used ChIP-seq to map Six4 binding profile in different C2C12 cell lines 24 hours after differentiation (T24). We performed ChIP-seq using two different antibodies: anti-Flag antibody in Flag-Six4 C2C12 cell line or in parental C2C12 cells; a custom-made anti-Six4 antibody in shNS C2C12 cell line (a control cell line) or shSix4 C2C12 (C2C12 with stable Six4 knockdown using short hairpin RNA). We also performed ChIP-seq in parental C2C12 cells using normal rabbit IgG. We were able to identify Six4-bound loci in C2C12 T24 that were recognized by two different antibodies and showed a decrease in peak intensity in shSix4 C2C12 compared to shNS C2C12 cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE66901 | GEO | 2015/12/31

SECONDARY ACCESSION(S): PRJNA278290

REPOSITORIES: GEO

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Genome-wide map of Six4 in C2C12 cells 24 hours post-differentiation

Project description:In this study, we used ChIP-seq to map Six4 binding profile in different C2C12 cell lines 24 hours after differentiation (T24). We performed ChIP-seq using two different antibodies: anti-Flag antibody in Flag-Six4 C2C12 cell line or in parental C2C12 cells; a custom-made anti-Six4 antibody in shNS C2C12 cell line (a control cell line) or shSix4 C2C12 (C2C12 with stable Six4 knockdown using short hairpin RNA). We also performed ChIP-seq in parental C2C12 cells using normal rabbit IgG. We were able to identify Six4-bound loci in C2C12 T24 that were recognized by two different antibodies and showed a decrease in peak intensity in shSix4 C2C12 compared to shNS C2C12 cells. We established a C2C12 cell line with stable Six4 knockdown by short hairpin RNA (shSix4) vs. a control cell line (shNS). We also established a C2C12 cell line with stable expression of Flag-Six4-myc by infection of retroviruses expressing pBABE-Flag-Six4-myc (Flag-Six4 C2C12) vs. parental C2C12. We differentiate these cells for 24 hours before using them for ChIP-seq.

2015-12-31 | E-GEOD-66901 | biostudies-arrayexpress

Gene expression profiling on C3H/10T1/2 fibroblasts during their myogenic conversion in case of Six4 ablation

Project description:In this study, we used C3H/10T1/2 cells, a well known model of myogenic conversion, to study the effect of Six4 knockdown on the expression of genes during fibroblasts to myocytes conversion induced by ectopic expression of MyoD We established C3H/10T1/2 cell line with stable Six4 knockdown by short hairpin RNA (shSix4) vs a control cell line (shLuc) and converted these cells into myogenic lineage by retroviral transduction of plasmid encoding Flag-MyoD-myc (pBABE-MyoD) or empty plasmid (pBABE). Cells were then induced to differentiate for 24 hours before RNA extraction.

2015-12-31 | E-GEOD-66319 | biostudies-arrayexpress

Gene Expression Profiling of siRNA Knock-Down of Six1, Six4 and Myogenin in C2C12

Project description:Six1, Six4 and Myogenin are transcription factors that are known to be required for skeletal myogenesis. Currently, very little is known about the genes targeted by Six1 and Six4. Gene expression profiling when one or both transcription factors were knock-down by siRNA was performed to identify genes affected by their absence. We also hypothesized that Six1 and Six4 can work in cooperation with the myogenic regulatory factor (MRFs) family of transcription factors, such as Myogenin. Therefore, we performed the same type of experiment where the myogenin was knocked-down by siRNA to identify genes that are possibly regulated by the Six1 or Six4 in conjunction with Myogenin. C2C12 Myoblasts were transfected with siRNA against Six1, Six4, Six1 with Six4, Myogenin, or control 24h before start of differentiation. The cells were allowed to differentiate in differentiation medium for 24h and were harvested for gene expression profiling. Four replicates per siRNA were performed.

2010-07-30 | E-GEOD-19967 | biostudies-arrayexpress

Gene Expression Profiling of siRNA Knock-Down of Six1, Six4 and Myogenin in C2C12

2010-07-05 | GSE19967 | GEO

SIX4 acts as a master regulator of genes associated with the malignant phenotype of non-small cell lung cancer cells

Project description:In this work, we evaluated SIX4, a member of the Homeobox gene, acts as a master regulator of oncogenes with the explicit function in the malignant phenotype of NSCLC cells. And SIX4 is a potential candidate of molecular marker for NSCLC.

2019-10-26 | GSE121866 | GEO

SIX1 and SIX4 homeoproteins regulate PAX7+ progenitor cell properties during fetal epaxial myogenesis

Project description:Identification of the gene targets of the SIX transcription factors in myogenic stem cells and in whole back muscles during murine fetal development Pax7 expression marks stem cells in developing skeletal muscles and adult satellite cells during homeostasis and muscle regeneration. The genetic determinants that control the entrance into the myogenic program and the appearance of PAX7+ cells during embryogenesis are poorly understood. SIX homeoproteins are encoded by the Sine oculis homeobox related Six1-Six6 genes in vertebrates. Six1, Six2, Six4 and Six5 are expressed in the muscle lineage. Here we tested the hypothesis that Six1 and Six4 could participate in the genesis of myogenic stem cells. We show that fewer PAX7+ cells occupy a satellite cell position between the myofiber and its associated basal lamina in Six1 and Six4 (s1s4KO) at E18. However, PAX7+ cells are detected in remaining muscle masses present in the epaxial region of the double mutant embryos and are able to divide and contribute to muscle growth. To further characterize the properties of s1s4KO PAX7+ cells, we analyzed their transcriptome and tested their properties after transplantation in adult regenerating tibialis anterior (TA) muscle. Mutant stem cells form hypotrophic myofibers that are not innervated but retain the ability to self-renew.

2020-10-07 | GSE159079 | GEO

Gene expression profiling on C3H/10T1/2 fibroblasts during their myogenic conversion in case of Six4 ablation

2015-12-31 | GSE66319 | GEO

LSD1 Corepressor Rcor2 Orchestrates Neurogenesis in the Developing Mouse Brain [ChIP-Seq]

Project description:ChIP-seq analysis using Flag M2, LSD1 and H3K4me2 antibodies respectively in Rcor2Flag embryonic brain.

2016-01-22 | GSE75039 | GEO

Genome-wide maps of chromatin state in C2C12 myoblast cells and myotubes.

Project description:We did ChIP-seq with anti- H3K4me3, H3K4me1, H3K4me2, H3K27me3, H3K27ac, and H3K36me3 antibodies in both C2C12 myoblasts and myotubes

2013-08-24 | GSE33227 | GEO

ChIP-Seq mapping of the genome-wide distribution of FLAG-H2AK5acK9ac in genetic code expanded HeLa cells

Project description:To test the deposition of FLAG-H2AK5acK9ac mark across the genome, ChIP experiments coupled high-throughput sequencing were performed using antibodies against FLAG, H2AK5ac and H2AK9ac. Keywords: Genome binding/occupancy profiling by high throughput sequencing

2024-02-16 | GSE252294 | GEO

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