Ontology highlight
ABSTRACT:
PROVIDER: PRJNA604277 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10997700_1.fastq.gz | Fastqsanger.gz | |||
| SRR10997700_2.fastq.gz | Fastqsanger.gz | |||
| SRR10997701_1.fastq.gz | Fastqsanger.gz | |||
| SRR10997701_2.fastq.gz | Fastqsanger.gz | |||
| SRR10997702_1.fastq.gz | Fastqsanger.gz |
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Project description:In order to identify how MnTE-2-PyP affects p300 association to chromatin genome-wide, we performed a p300 chromatin Immunoprecipitation assay followed by Next Generation Sequencing on PC3 cells treated with or without MnTE-2-PyP one hour post-irradiation (Figure 3A). Based on the called peaks near genes, we predicted that HIF-1βand CREB transcription factors were associating DNA less in the presence of MnTE-2-PyP. DNA was ChIP-Fixed from Pc3 cells treated with 20 Gy radiation and with and without T2E drug. There are 2 biological replicates of PC3 untreated cells and 3 biological replicates of PC3 cells treated with MnTE-2-PyP. There are two corresponding input samples for the biological replicates.
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Project description:A whole genome screen using a CRISPR lentivirus library (Doench et al., 2016) was performed. The Brunello CRISPR library consists of a pool of 76,441 human targeting guide RNAs (gRNA) and 1000 control gRNAs [non-targeting (NT) or intergenic], in a lentiviral vector that expresses Cas9. The pooled library targets 19,114 human genes, most of them by four gRNA per gene. To avoid multiple different gRNA in cells and a nonspecific effect on the screen results (Doench, 2018), a low infection lentivirus titer (multiplicity of infection that is <1) was used. Library transduced cells (LT SC-islets) were allowed at least 10 days for CRISPR editing, before transplantation to the NSG-MHCnull mouse model, where PBMCs were injected to half of the cohort (hPi mice: n=6, control mice: n=6) (Figures 3A). hPi mice retained levels of circulating T cells throughout the experiment (Figures S3A and S3B). Graft function and subsequent failure due to human PBMC injection was assessed (Figures 3B and S3C). When hPi graft failure was confirmed, 10 weeks after PBMC injection (Figure 3B), both control and hPi grafts were recovered from kidney sites, genomic DNA (gDNA) was extracted, and gRNA regions were amplified by PCR for Illumina sequencing.
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