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Homo sapiens

ABSTRACT: RNAseq to determine gene expression changes following depletion of SETDB1 in THP-1 AML Cells

PROVIDER: PRJNA401801 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6000440.fastq.gz	Fastqsanger.gz
	SRR6000431.fastq.gz	Fastqsanger.gz
	SRR6000441.fastq.gz	Fastqsanger.gz
	SRR6000432.fastq.gz	Fastqsanger.gz
	SRR6000442.fastq.gz	Fastqsanger.gz

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Similar Datasets

Homo sapiens

Project description:RNAseq to determine whether bidirectional transcription occurs over transposable elements following depletion of SETDB1 in THP-1 AML Cells

| PRJNA401800 | ENA

RNAseq to determine whether bidirectional transcription occurs over transposable elements following depletion of SETDB1 in THP-1 AML Cells

Project description:SETDB1 disruption leads to an increase in the expression of transposable elements as determined by our standard RNAseq, where bidirectional transcription has been reported. We repeated RNA seq on our samples with a stranded prep to determine whether bidirectional transcription occurs of transposable elements following depletion of SETDB1 in THP-1 AML Cells Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. RNA was isolated and prepared for RNAseq with Qiagen RNeasy kits. Results: Consensus sequences for elements for upregulated TEs were downloaded from the Dfam database (Hubley et al., 2016). Stranded RNA-seq data was then aligned to consensus sequences using BWA-MEM and quantified using HTseq-count(Anders et al., 2015; Li, 2013). Reads were visualized using the IGV genome browser, using a custom pseudogenome that was generated from the Dfam consensus sequences (Robinson et al., 2011; Thorvaldsdottir et al., 2013). Conclusions: Our data determined that following the disruption of SETDB1, there is increased bidirectional transcription over a subset of transposable elements.

2017-09-06 | GSE103410 | GEO

RNAseq to determine gene expression changes following depletion of SETDB1 in THP-1 AML Cells

Project description:Purpose: To determine how loss of SETDB1 effects gene expression in THP-1 AML cells. Methods: THP-1 cells were treated with two different SETDB1 sgRNAs (6, and 9) or Non-targeting control sgRNA (NTC) for 4 and 7 days. RNA was isolated and prepared for RNAseq with Qiagen RNeasy kits. Results: Using an optimized data analysis workflow, we mapped 23 million or more sequence reads per sample to the human genome (GRCh38) with GSNAP for obtaining standard gene expression measurements. Since SETDB1 is also know to regulate repetitive elements we also mapped sequences to a pseudogenome containing tranposable elements from hg19 repeatmasker annotations using RepEnrich and following the pipeline published on GitHub (https://github.com/nskvir/RepEnrich). Conclusions: Our data determined that immediately following the disruption of SETDB1, a strong type I Interferon response can be observed at day 4. In addition, many repetitive elements are also significanly induced, including L1 LINEs, Endogenous Retroviruses, and Satellite repeats.

2017-09-06 | GSE103409 | GEO

Histone demethylase KDM4A-mediated promotion of PAF1/NFATC2 expression is required for oncogenesis in MLL-AF9 acute myeloid leukemia [RNA-seq]

Project description:In this study we identified the histone demethylase KDM4A as an essential and selective regulator of AML oncogenic potential. RNAseq was used to follow the changes in gene expression following KDM4A knockdown in MLL-AF9 human AML THP-1 cells

2021-01-17 | GSE125374 | GEO

Homo sapiens immortalized MSCs: 3A6

Project description:Gene expression profiling of immortalized human mesenchymal stem cells with hTERT/E6/E7 transfected MSCs. hTERT may change gene expression in MSCs. Goal was to determine the gene expressions of immortalized MSCs.

2010-09-25 | GSE24338 | GEO

Homo sapiens MSCs: Normoxia vs. Hypoxia

Project description:Transcriptional profiling of human mesenchymal stem cells comparing normoxic MSCs cells with hypoxic MSCs cells. Hypoxia may inhibit senescence of MSCs during expansion. Goal was to determine the effects of hypoxia on global MSCs gene expression.

2011-02-19 | GSE20463 | GEO

Kynurenine engages Serotonin Receptor 1b in osteoblasts to reinforce Acute Myeloid Leukemia

Project description:We performed RNAseq analysis of primary human osteoblasts co-cultured with the human THP-1 AML cell-line and, in parallel, RNAseq analysis on the THP-1 AML cells exposed to the human primary osteoblasts.

2020-07-15 | GSE154374 | GEO

Homo sapiens immortalized MSCs: KP vs. 3A6

Project description:Gene methylation profiling of immortalized human mesenchymal stem cells comparing HPV E6/E7-transfected MSCs cells with human telomerase reverse transcriptase (hTERT)- and HPV E6/E7-transfected MSCs. hTERT may increase gene methylation in MSCs. Goal was to determine the effects of different transfected genes on global gene methylation in MSCs.

2011-08-25 | GSE23936 | GEO

Homo sapiens immortalized MSCs: 3A6

2010-09-25 | E-GEOD-24338 | biostudies-arrayexpress

Crystal structure of Homo sapiens kynureninase.

Project description:Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.

| S-EPMC2531291 | biostudies-literature

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