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Ribo-Seq timecourse in RAW264.7 cells upon LPS treatment

ABSTRACT: Ribo-Seq timecourse in RAW264.7 cells upon LPS treatment

PROVIDER: PRJNA649003 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12333531.fastq.gz	Fastqsanger.gz
	SRR12333532.fastq.gz	Fastqsanger.gz
	SRR12333533.fastq.gz	Fastqsanger.gz
	SRR12333534.fastq.gz	Fastqsanger.gz
	SRR12333535.fastq.gz	Fastqsanger.gz

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Ribo-Seq timecourse in RAW264.7 cells upon LPS treatment

Project description:mRNAs are generally assumed to be loaded instantly with ribosomes upon entry into the cytoplasm. To measure ribosome density on nascent mRNA, we developed nascent Ribo-Seq (nRibo-Seq) by combining Ribo-Seq with progressive 4-thiouridine labelling. In mouse macrophages, we experimentally determined, for the first time, the lag between the appearance of nascent RNA and its association with ribosomes, which was calculated to be 20 - 22 min for bulk mRNA, and approximated the time it takes for mRNAs to be fully loaded with ribosomes to be 41 - 44 min. Notably, ribosomal loading time is adapted to gene function as rapid loading was observed with highly regulated genes. The lag and ribosomal loading time correlate positively with ORF size and half-life, and negatively with tRNA adaptation indices. Similar results were obtained in mESCs, where the lag between IN and FP was even more pronounced with 35 - 38 min. We validated our measurements after stimulation of macrophages with lipopolysaccharide, where the lag between cytoplasmic and translated mRNA leads to a corresponding uncoupling between input and ribosome-protected fragments. Uncoupling is stronger for mRNAs with long ORFs or half-lives, a finding we also confirmed at the level of protein production by nascent chain proteomics. As a consequence of the lag in ribosome loading, ribosome density measurements are distorted when performed under conditions where mRNA levels are far from steady state expression, and transcriptional changes affect ribosome density in a passive way. This study uncovers an unexpected and considerable lag in ribosome loading, and provides guidelines for the interpretation of Ribo-Seq data taking passive effects on ribosome density into account.

2021-06-23 | GSE155233 | GEO

ActD timecourse in RAW264.7 cells

Project description:ActD timecourse in RAW264.7 cells

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H3K4methylation in Setd1a loss-of-function Raw264.7 cells upon LPS or Dex+LPS stimulation

Project description:H3K4methylation in Setd1a loss-of-function Raw264.7 cells upon LPS or Dex+LPS stimulation

| PRJNA574157 | ENA

nRibo-Seq timecourse in RAW264.7 cells

Project description:nRibo-Seq timecourse in RAW264.7 cells

| PRJNA649002 | ENA

H3K4methylation in Setd1a loss-of-function Raw264.7 cells upon LPS or Dex+LPS stimulation

Project description:Nuclear interaction studies by ChIP coupled with mass spectrometry identified the COMPASS/SETD1A complex as interaction partner of the glucocorticoid receptor (GR) in murine bone marrow-derived macrophages (BMDMs). Here, we profiled H3K4me1, H3K4me2 and H3K4me3 in wild-type and Setd1a hypermorphic (Setd1aDel/+) Raw264.7 cells after LPS and Dex+LPS stimulation by spike-in ChIP-Seq.

2020-12-31 | GSE138017 | GEO

AF9/MLLT3 ChIP-Seq in LPS-stimulated RAW264.7 cells

Project description:We sought to characterize the genomic localization of the YEATS domain protein AF9 in the macrophage-like cell line RAW 264.7 +/- LPS stimulation and +/- sodium crotonate pretreatment. We performed chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-seq) for endogenous AF9 or for a FLAG-tagged AF9 transgene in RAW264.7 or a RAW264.7 cell line engineered to express FLAG-AF9, respectively.

2016-04-21 | GSE76539 | GEO

High-throughout sequencing of RAW264.7 cells treated with LPS and Harmine

Project description:After stimulation of RAW264.7 cells with LPS and Harmine, high-throughput sequencing technology was used to explore the changes in the inflammation level of RAW cells and the enrichment of signaling pathways after LPS and Harmine treatment, and to find an interesting target pathway.

2024-05-20 | GSE267507 | GEO

RNA-seq in RAW264.7 cells after silence of Synbindin in response to LPS

Project description:RAW264.7 cells were transfected with Synbindin siRNA for 48hours, then 100ng/ml LPS were treated cells for 4 hours. Before and after LPS stimulation, cells were collected and RNA were extracted for RNA-seq.

2022-09-01 | GSE158301 | GEO

Ribosome profiling (Ribo-Seq) and mRNA sequencing (RNA-Seq) of Human leukemia monocytic cell line (THP-1) cells upon treatment with LPS and LPS+dexamethasone (Dex).

Project description:THP-1 cells were treated with vehicle control (0.1% ethanol/PBS), LPS and LPS+Dex for 3 hr. We then performed combined analysis of ribosome footprints (RPF) and mRNA abundance using the data obtained by Ribo-Seq and RNA-seq in THP-1 cells.

2022-10-06 | GSE208041 | GEO

Deep chemoproteomic analysis of LPS-stimulated RAW264.7 cell proteome

Project description:Unanticipated regulatory protein modifications can be discovered from the unbiased comprehensive analysis of biological systems using SAMPEI. To explore this idea, we sought to map protein modifications induced during mammalian cell differentiation, modeled by the response of mouse RAW264.7 macrophage cells to lipopolysaccharide (LPS), a potent inducer of macrophage activation and differentiation that involves extensive protein and metabolic signaling.

2021-07-22 | PXD019853 | Pride

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