ABSTRACT: ChIP-seq after immunoprecipitation with either IgG or SOX2 antibodies in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells)
Project description:SOX2 is the main gene involved in anophthalmia. In order to identify genes regulated by SOX2 transcription factors (genes that could be good candidates to also be involved in ocular development), we studied transcriptomic profiles of murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA. murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA
Project description:In order to identify target genes of the SOX2 transcription factor, we tried to identify SOX2 binding site in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) by ChIP-seq. SOX2 gene mutations are involved in anophthalmia and our hypothesis was that target genes of SOX2 transcription factor may also be candidate to be involved in ocular development. High throughput sequencing after chromatin immunoprecipitation using either an antibody against our target transcription factor (SOX2) or using control antobodies (IgG). These experiments were performed on only one immunoprecipitation with each antibody.
Project description:SOX2 is the main gene involved in anophthalmia. In order to identify genes regulated by SOX2 transcription factors (genes that could be good candidates to also be involved in ocular development), we studied transcriptomic profiles of murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) after transfection by a siRNA against SOX2 or a scramble siRNA.
Project description:In order to identify target genes of the SOX2 transcription factor, we tried to identify SOX2 binding site in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) by ChIP-seq. SOX2 gene mutations are involved in anophthalmia and our hypothesis was that target genes of SOX2 transcription factor may also be candidate to be involved in ocular development.
Project description:Transcriptomic analysis after transfection in murine genetically modified stem cells overexpressing the RAX gene (CCE-Rx cells) of either a siRNA against SOX2 or a scramble siRNA
| PRJNA300947 | ENA
Project description:Transcriptomic analysis and ChIP-seq in CCE-Rx cells to identify SOX2 transcription factor target genes
Project description:To gain insight into the specificity of target mRNAs, we enriched mRNAs bound to TRS by immunoprecipitation with anti-TRS antibody, then performed RNA immunoprecipitation and sequencing (RIP-seq) and compared the mRNAs with those enriched by immunoprecipitation with IgG, anti-AlaRS, anti-PRS and anti-IRS antibodies.
Project description:Immunoprecipitation was performed with HCT116 cells overexpressing 3xFLAG-SET/TAF-Ib with anti-FLAG antibodies. The immunoprecitates were separated by SDS-PAGE and putative interaction partners of SET/TAF-Ib were identified with mass spectrometry.
Project description:Genetically modified ovarian cancer cells were used to study the role of GBP1. Proteomics-based thermal stability assay (CETSA) was performed on GBP1 knockdown and overexpressing ID8 ovarian cancer cells. Shotgun proteomics was also performed on these cells.
Project description:To identify the MYCN transcription factor binding sites across the genome, we performed chromatin immunoprecipitation followed by sequencing (ChIP-seq) using anti-MYCN and anti-IgG antibodies on a MYCN-amplified NB cell line, SK-N-BE(2)-C.
