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RNA-seq of ER-targeted and cytosolic mRNAs with control or CNOT1-targeting siRNA treatment in HEK293 cells

ABSTRACT: Determination of mRNA localisation in HEK293 cells with and without the depletion of CNOT1

ORGANISM(S): Homo sapiens

PROVIDER: GSE183148 | GEO | 2021/09/07

REPOSITORIES: GEO

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Project description:Gene expression is balanced by transcription and mRNA degradation. Shortening of polyadenosine (poly(A)) tails (deadenylation) is the initial step in the decay of most mRNAs. However, the mechanism by which deadenylation controls mRNA expression is not fully understood. This experiment aimed to determine changes in transcriptional activity in livers of control and Cnot1 tamoxifen-inducible liver-specific knockout mice. Control and Cnot1 tamoxifen-inducible liver-specific knockout mice placed on tamoxifen-containing food at 6 weeks of age for 2 weeks. Lysates from livers were subjected to ChIP assay with Histone H3 (tri methyl K4) (H3K4me3) antibody (ab8580; abcam) using SimpleChIP Enzyatic Chromatin IP Kit (#9003; Cell Signaling Technology). Libraries for DNA sequence were prepared from DNA isolated by ChIP assays with a KAPA Hyper Prep Kit (Illumina). 109 base-pair pair-end read DNA-seq was performed with Hiseq PE Rapid Cluster Kit v2-HS and Hiseq Rapid SBS Kit v2-HS (200 Cycle) on Illumina Hiseq2500.

2020-03-30 | E-MTAB-5887 | biostudies-arrayexpress

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Project description:Gene expression is balanced by transcription and mRNA degradation. Shortening of polyadenosine (poly(A)) tails (deadenylation) is the initial step in the decay of most mRNAs. However, the mechanism by which deadenylation controls mRNA expression is not fully understood. This experiment aimed to determine changes in gene expression and mRNA stability in livers of control and Cnot1 tamoxifen-inducible liver-specific knockout mice. For comprehensive mRNA half-life profiling, we injected control and Cnot1 tamoxifen-inducible liver-specific knockout mice, which were placed on a tamoxifen-containing diet at 6 weeks of age for 2 weeks, intraperitoneally with 2 mg actinomycin D per g body weight for 4 and 8 hr. 1 g of total RNA was used for RNA-seq library preparation with Illumina TruSeq Stranded mRNA LT Sample Prep Kit. 109 base-pair pair-end read RNA-seq was performed with Hiseq PE Rapid Cluster Kit v2-HS and Hiseq Rapid SBS Kit v2-HS (200 Cycle) on Illumina Hiseq2500.

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