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Repeat elements analysis of Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblasts using RNA-Seq

ABSTRACT: Repeat elements analysis of Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblasts using RNA-Seq

PROVIDER: PRJNA680164 | ENA |

REPOSITORIES: ENA

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Repeat elements analysis of Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblasts using RNA-Seq

Project description:RNA sequencing of Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblasts. Total RNA was sequenced to analyse noncoding transcripts and repeats

2021-05-01 | GSE161964 | GEO

Actb knockout in primary mouse embryonic fibroblasts LC-MS/MS

Project description:The cytoplasmic actin proteins, beta- and gamma-actin, are 99% identical but perform non-redundant functions. Genes encoding the cytoplasmic actins, Actb and Actg1, respectively, are less similar but still share 89% of their nucleotide sequences. Knockout (KO) of Actb by deletion of first coding exons 2 and 3 in mice is embryonic lethal while KO embryonic fibroblasts (MEFs) fail to proliferate. In contrast, KO of Actg1 is viable but mice lacking Actg1 present with increased perinatal lethality and Actg1 KO MEFs present with a much milder defect in cell proliferation. Recent studies have identified important protein-independent functions for both Actb and Actg1 and demonstrate that deletions within the Actb nucleotide sequence, and not loss of the beta-actin protein, cause the most severe phenotypes in KO mice and cells. Here, we use a multi-omics approach to better understand what drives the phenotypes of Actb KO MEFs. RNA-sequencing and mass spectrometry of Actb KO MEFs reveal largescale changes to the transcriptome, proteome, and phosphoproteome. Pathway analysis of genes and proteins differentially expressed upon Actb KO shows widespread dysregulation of genes involved in the cell cycle. Together, these data suggest novel, protein-independent roles for Actb in regulating gene expression associated with control of cell proliferation.

2024-02-19 | PXD039786 | Pride

Next-generation sequencing analysis of chemically induced neurons from wild type (WT), Actb+/- (HET) and Actb-/- (KO) mouse embryonic fibroblasts (MEFs)

Project description:Purpose: The goals of this study are to use NGS to perform transcriptome profiling (RNA-seq) to find the difference of the transcriptomes of chemically induced neurons from wild type (WT), Actb+/- (HET) and Actb-/- (KO) mouse embryonic fibroblasts. Methods: MEFs were reprogramed into neurons by small chemical cocktails. Small chemical molecules were dissolved and diluted in DMSO and used at the following final concentrations: ISX9: 20 mM; Forskolin: 50 mM; CHIR99021: 20 mM; and I-BET151: 2 mM. In addition to the small molecules, the neuron induction medium (Neurobasal Medium) contains the following supplements: N2 (1X) and B27 (2X) supplements, GlutaMAX (1X), penicillin-streptomycin (100 µg/ml), bFGF (20 ng/ml), 100 µM cAMP, Non-essential Amino Acid (1X) and Trace element B (1X). MEFs were seeded to Matrigel-coated plate (1:30 dilution in pre-cold PBS and coat overnight at 4 oC, at a density of 200,000 cells per well in 6-well plate and 10,000 cells/well in 96 well plate. The MEFs were cultured in DMEM until confluent. When the cells are confluent, the DMEM was replaced with neuron induction medium with 4 small molecules. The induction medium was refreshed every two days for the first week and every 3 days for the remaining induction period until day 20. 3 biological replicates of total RNA were used for RNA-seq library preparation. Results: Using an optimized data analysis workflow, we identified neuronal gene programs induced during direct reprograming. The induction of neuronal programs were impaired in neurons from Actb-/- mouse embryonic fibroblasts. Conclusions: Our study shows that neuronal program induction was impaired in chemically induced neurons from Actb-/- mouse embryonic fibroblasts.

2018-04-27 | GSE113733 | GEO

TFAM binding analysis at mitochondrial genome between Wild Type (Wt) and Actb-/- (KNO) Mouse Embryonic Fibroblast

Project description:Using Chromatin-immunoprecipitation and NGS, we investigated the binding of TFAM protein at mitochondrial genome between Actb+/+ Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblast

2018-01-24 | GSE109532 | GEO

Next-generation sequencing analysis of chemically induced neurons from wild type (WT), Actb+/- (HET) and Actb-/- (KO) mouse embryonic fibroblasts (MEFs)

Project description:Next-generation sequencing analysis of chemically induced neurons from wild type (WT), Actb+/- (HET) and Actb-/- (KO) mouse embryonic fibroblasts (MEFs)

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Genome-wide ChIP-Seq maps of EZH2 distribution between Wild Type (WT), Actb+/- (HET), and Actb-/- (KO) Mouse Embryonic Fibroblast

Project description:Genome-wide ChIP-Seq maps of EZH2 distribution between Wild Type (WT), Actb+/- (HET), and Actb-/- (KO) Mouse Embryonic Fibroblast

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ChIP-Seq of H3K27ac in Wild Type (WT), and Actb-/- (KO) Mouse Embryonic Fibroblasts

Project description:Genome-wide ChIP-Seq of H3K27ac in WT and β-actin KO MEFs to assess the role of nulcear actin in regulating histone acetylation

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Genome-wide maps of H3K9Me3, H3K27Me and Brg1 distribution between Wild Type (Wt) and Actb-/- (KNO) Mouse Embryonic Fibroblast

Project description:Using Chromatin-immunoprecipitation and NGS, we profiled the genome-wdie H3K9Me3, H3K27Me and Brg1 distribution between Wild Type (Wt) and Actb-/- (KNO) Mouse Embryonic Fibroblast

2017-07-01 | GSE100096 | GEO

RNA-RNA interaction analysis of functional SINE repeat elements-derived transcripts

Project description:We studied functional and structural features of mouse and human SINE repeat elements-derived RNAs in SINEUP long non-coding RNAs which upregulate the translation of the target protein coding gene. To check the interaction of functional SINE RNAs with ribosomal RNAs, we created PARIS2 (psoralen analysis of RNA interactions and structures) libraries from SINEUP (with embedded mouse SINEB2 or human FRAM repeat) and the target sense GFP plasmids co-transfected human cells.

2023-02-06 | GSE224533 | GEO

Genome-wide ChIP-Seq maps of REST distribution in Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblast

Project description:Genome-wide ChIP-Seq maps of REST distribution in Wild Type (WT) and Actb-/- (KO) Mouse Embryonic Fibroblast

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