Project description:Purpose: The Goal of this study is to look at 1) Differences in genome wide localization of Scc2 between wild type and scc4-m35 cells in S-phase 2) Differences in genome wide localisation of Scc1 cohesin between wild type and scc4-m35 in metaphase arrested cells. Method: 1) Wild-type (AM15307) and scc4-m35 (AM15311) cells carrying SCC2-3FLAG were fixed for 2 hr, 15 min following an a-factor arrest. Samples were harvested, anti-HA ChIP was performed and both input and IP samples were sequenced for both strains. 2) Wild-type (AM1145), wild type constructed in the same way as the mutant strain (carrying a HIS3 marker) (AM15540) and scc4-m35 mutant (AM15537) cells carrying SCC1-6HA were synchronised with a-factor and arrested in mitosis by treatment with nocodazole/benomyl for 2 hr. Samples were harvested, anti-HA ChIP was performed and input and IP samples were sequenced for the three strains. Results: 1) This experiment did not yield meaningful data. 2) All 16 centromeres were specifically depleted of Scc1 in the scc4-m35 background. Scc1 depletion extended roughly 10 kilobases to either side of the core centromere but not to chromosome arms 1) ChIP-seq for S. cerevisiae Scc2-3FLAG in S-phase cells in Wild type and in scc4-m35 mutant (samples VM1-VM4). 2) ChIP-seq for Scc1-6HA in metaphase-arrested cells in Wild type and in scc4-m35 mutant (samples VM5-VM10) Vasso Makrantoni: experiments and Alastair Kerr: ChIP Seq Data analysis https://github.com/AlastairKerr/Hinshaw2015

2015-06-05 | E-GEOD-68573 | biostudies-arrayexpress

Structural evidence for Scc4-dependent localization of cohesin loading

Project description:Purpose: The goal of this study is to look at differences in genome wide localisation of Scc1 cohesin between wild type and scc4-m35 in metaphase arrested cells. Method: Wild-type (AM1145), wild type constructed in the same way as the mutant strain (carrying a HIS3 marker) (AM15540) and scc4-m35 mutant (AM15537) cells carrying SCC1-6HA were synchronised with a-factor and arrested in mitosis by treatment with nocodazole/benomyl for 2 hr. Samples were harvested, anti-HA ChIP was performed and input and IP samples were sequenced for the three strains. Results: All 16 centromeres were specifically depleted of Scc1 in the scc4-m35 background. Scc1 depletion extended roughly 10 kilobases to either side of the core centromere but not to chromosome arms

2015-06-05 | GSE68573 | GEO

localization of Scc2 between wild type and scc4-m35 cells in S-phase

Project description:Wild-type (AM15307) and scc4-m35 (AM15311) cells carrying SCC2-3FLAG were fixed for 2 hr, 15 min following an a-factor arrest. Samples were harvested, anti-HA ChIP was performed and both input and IP samples were sequenced for both strains. ChIP-seq for S. cerevisiae Scc2-3FLAG in S-phase cells in Wild type and in scc4-m35 mutant Vasso Makrantoni: experiments and Alastair Kerr: ChIP Seq Data analysis

2016-07-21 | E-GEOD-70316 | biostudies-arrayexpress

Gene expression profiling of TH-MYCN mouse neuroblastoma sphere cells and their parental primary tumor cells

Project description:We performed microarray gene expression profiling to identify genes essential for the growth and tumorigenicity of mouse neuroblastoma stem-like cells Affymetrix microarray assays were performed according to the manufacturer's directions on total RNA isolated from three independent lines of mouse neuroblastoma sphere cells and their parental primary tumor cells

2016-08-24 | E-GEOD-80252 | biostudies-arrayexpress

RNAseq Analysis Investigates Transcriptional Similarities and Differences Between Cryopreserved Parental and Engineered iPSC Derived Macrophages

Project description:RNAseq Analysis Investigates Transcriptional Similarities and Differences Between Cryopreserved Parental and Engineered iPSC Derived Macrophages

| PRJNA718884 | ENA

localization of Scc2 between wild type and scc4-m35 cells in S-phase

2016-07-21 | GSE70316 | GEO