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FLAG RIP-Seq identifies RNA species bound by cytoplasmic TAF7 in HeLa TAF7 (WT) cells

ABSTRACT: FLAG RIP-Seq identifies RNA species bound by cytoplasmic TAF7 in HeLa TAF7 (WT) cells

PROVIDER: PRJNA679052 | ENA |

REPOSITORIES: ENA

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FLAG RIP-Seq identifies RNA species bound by cytoplasmic TAF7 in HeLa TAF7 (WT) cells

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anti-TAF7 RIP-Seq identifies RNA species bound by cytoplasmic TAF7 in HeLa TAF7 (WT) cells

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anti-TAF7 RIP-Seq identifies RNA species bound by cytoplasmic TAF7 in HeLa TAF7 (WT) cells

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Identify Flag-bound transcripts via RIP-seq

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RIP-chip of HuR in MCF7 cells exposed to doxorubicin

Project description:The purpose of the study was to identify mRNA bound to HuR in the presence of doxorubicin in MCF7 cells. We collected cytoplasmic RNA from untreated and treated cells and detected differentially expressed genes (DEGs). We also coimmunoprecipitated HuR and IgG (as control) from doxorubicin treated cells. Comparison between HuR RIP and IgG RIP signals was used to discriminate specific mRNA bound to HuR. HuR coimmmunoprecipitated material was hybridized together with cytoplasmic mRNA of doxorubicin treated cells, enabling the fold enrichment calculation and the selection of mRNAs bound to HuR. Keywords: RIP-Chip, HuR, doxorubicin, MCF7, HuR consensus binding, post-transcriptional regulation. We subjected MCF7 cells to starvation for 24h and then we added doxorubicin at final concentration of 10 uM, profiling before and after 4 hours of treatment in biological quadruplicate (only on cytoplasmic mRNAs, as HuR was found in the cytoplasm). Differentially expressed genes, altered during the treatment, were identified. Data derived from HuR RIP-Chip and IgG RIP-Chip (in biological quadruplicate) allowed the identification of specific mRNAs bound to HuR. The comparison between HuR RIP-Chip and cytoplasmic extracts from doxorubicin treated cells (in biological triplicate) identified those genes that were more strictly bound to HuR independently from their expression levels.

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