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RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 or human embryonic kidney cell line HEK293 via the dTAG degron system

ABSTRACT: RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 or human embryonic kidney cell line HEK293 via the dTAG degron system

PROVIDER: PRJEB72831 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR12684127_1.fastq.gz	Fastqsanger.gz
	ERR12684127_2.fastq.gz	Fastqsanger.gz
	ERR12684128_1.fastq.gz	Fastqsanger.gz
	ERR12684128_2.fastq.gz	Fastqsanger.gz
	ERR12684129_1.fastq.gz	Fastqsanger.gz

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Rapid UPF1 depletion illuminates the temporal dynamics of the NMD-regulated human transcriptome

Project description:UPF1 is a multi-domain RNA helicase that constantly monitors the transcriptome by non-specifically binding to mRNAs, dissociating from non-target transcripts, and initiating degradation on selected target RNAs via multiple proposed pathways such as nonsense-mediated decay (NMD). NMD is a translation-coupled mechanism that targets mRNAs harboring a premature stop codon (PTC) for degradation, thereby serving as a quality control and gene regulatory pathway ensuring transcriptome integrity. The UPF1 gene is essential in cultured human cells and previous studies relied mostly on RNA interference to downregulate UPF1. Here we established an auxin-inducible UPF1 degron system in the human colorectal adenocarcinoma cell line HCT116 by first inserting the auxin receptor F-box protein-encoding AtAFB2-mCherry in the AAVS1 locus, followed by tagging UPF1 at the N-terminus with an V5-AID-tag (AID = miniIAA7 = AtIAA7 amino acids 37–104). With this cell line we wanted to explore the time-resolved proteomic changes upon rapid depletion of UPF1. To this end, depletion of UPF1 was induced with 500 µM indole-3-acetic acid (IAA) for various time periods (0-24h). As controls, the cells were treated for the same time with DMSO.

2025-09-03 | PXD061797 | Pride

SLAM-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

Project description:SLAM-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

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Ribo-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

Project description:Ribo-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

| PRJEB80386 | ENA

RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

Project description:RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

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RNAPII interactome in INTS6 degron cells

Project description:In this study we show that acute INTS6 depletion remodels the RNAPII interactome and enhances ARMC5 binding, the same as what we observed in Ints6 KO cells. To investigate how acute INTS6 depletion affects RNAPII function, we determined the RNAPII interactome in the the Ints6 degron cells. Chromatin fractions from DMSO and dTAG treated Ints6 degron cells (treated for 1 hour) were analyzed by RNAPII IP-mass spectrometry. There are 12 samples in this MS run, samples 6-dTAG repeats1-3 and 6-DMSO repeats 1-3 are involved in the paper.

2025-12-22 | PXD053351 | Pride

RiboMinus RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

Project description:RiboMinus RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

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Initial Test-RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

Project description:Initial Test-RNA-Seq of UPF1 depletion in human colorectal adenocarcinoma cell line HCT116 via the auxin-inducible degron (AID) system

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RNA-Seq of UPF1 recovery in human colorectal adenocarcinoma cell line HCT116 previously depleted via the auxin-inducible degron (AID) system

Project description:RNA-Seq of UPF1 recovery in human colorectal adenocarcinoma cell line HCT116 previously depleted via the auxin-inducible degron (AID) system

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SF3B1 Degron knockdown RNA-seq

Project description:Knockdown of mutant and/or wild-type SF3B1 in MEL202 cell line by Degron knock-in, followed by RNA-seq, to identify splicing events governed by mutant SF3B1. Control: parental MEL202 cell line. Experiments: mutant-SF3B1 knockdown; wildtype-SF3B1 knockdown; mutant SF3B1 knockout. Treatments: each of these four conditions plus and minus shld.

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UPF1 knockdown in differentiating human myoblasts

Project description:Human myoblast cell line 54-1 is transfected with either a srambled control siRNA or siRNA against UPF1. Two days after transfection, cell were induced to differentiate by changing grow meida to differentiation media. 2 days after induction of differentiation, cells are collected for extraction of RNA.

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