Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Critical Role of Nuclear m6A Reader YTHDC1 in Leukemogenesis by Regulating MCM Complex-Mediated DNA Replication

ABSTRACT: PLKO.1 lentiviral vectors contained scramble shRNA, YTHDC1 shRNA 1# and YTHDC1 shRNA 2# were transfected into 293T cells together with package plasmids pMDG.2 and Δ8.91. The supernatant medium contained virus was collected and subjected to infect MOLM-13 cells by spinoculation, MOLM-13 cell is an AML cell line. The positive cells were collected 3 days after viral infection and subjected to RNA-seq.

ORGANISM(S): Homo sapiens

PROVIDER: GSE178859 | GEO | 2021/06/25

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

PAR-CLIP analysis of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 in human HeLa cells

Project description:Label the cells overexpressed Flag tagged YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 and SRSF10 with 4-SU, the RNA bound by YTHDC1 and SRSF proteins can be got by Flag IP followed by RNA isolation by using the TRIzol (Invitrogen) reagent by following the company manual.the RNA was then used for library preparation using a TruSeqâ¢ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturerâs protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane. Discovery of the binding motif of YTHDC1, SRSF1, SRSF3, SRSF7, SRSF9 or SRSF10 in overexpressed Human HeLa cells

2016-02-17 | E-GEOD-71096 | biostudies-arrayexpress

YTHDC1 m6A-dependent and m6A-independent functions converge to preserve DNA damage response (Ythdc1 ChIP-Seq)

Project description:Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding of its impact on a fully efficient DNA damage response remains limited. Here, through a targeted CRISPR-knockout screen, we identified RNA binding proteins and modifiers that participate in mediating the p53 response. Among the top hits, m6A reader YTHDC1 was identified as a master regulator of p53 expression. YTHDC1 binds to the transcription start sites ofTP53and other genes involved in DNA damage response, promoting their transcriptional elongation. YTHDC1 deficiency leads to reducedTP53expression, and also retention of introns leading to aberrant protein production of key DNA damage factors. While intron retention is dependent on m6A, YTHDC1 favoursTP53transcriptionalpause-release independently of m6A. Depletion of YTHDC1 causes genomic instability and aberrant cancer cell proliferation mediated by genes regulated by YTHDC1. Our results uncover YTHDC1 as an orchestrator of the DNA damage response through distinct mechanisms of co-transcriptional mRNA regulation.

2024-05-07 | GSE239331 | GEO

YTHDC1 regulate hematopoietic stem cell survival and regeneration

Project description:we investigate the role of YTHDC1 in normal hematopoiesis and adult hematopoietic stem/progenitor cell (HSPC) maintenance in vivo. Utilizing conditional Ythdc1 knockout mice ,we show that YTHDC1 is required for hematopoietic stem cell (HSC) maintenance as well as self-renewal of HSC. Transcriptome analysis identified many differentially expressed genes (DEGs) between WT and YTHDC1-KO LT-HSCs.

2023-07-01 | GSE208626 | GEO

YTHDC1-Hyper tribe uncover YTHDC1 binding sites in human leukemia cells

Project description:The goal of this study is to identify YTHDC1 binding targets in MOLM13 cells(AML).

2021-05-24 | GSE168568 | GEO

Microarray transcription analysis of MDS/MPN leukocyte samples with and without EZH2 mutations (n = 12, each) and EZH2-downregulated F-36P, MOLM-13 and OCI-M2 cell lines, using 2 shRNAs targeting EZH2 and a non-targeting control shRNA, each

Project description:The aim of this study was to identify EZH2 targets in myeloid malignancies. RNA samples from control F-36P, MOLM-13 and OCI-M2 cells (secondary AML after MDS; EZH2 wild type) treated with random shRNA (n = 4, each) and test F-36P, MOLM-13 and OCI-M2 cells treated with either one of two EZH2-targeting shRNAs (n = 4, each) were screened for differential gene expression. RNA from EZH2 wild type (n = 12) and mutant (n = 12) MDS/MPN patients was also analyzed by microarray transcriptome analysis.

2017-06-15 | E-MTAB-5766 | biostudies-arrayexpress

MS-based characterization of YTHDC1 interactome

Project description:Heat shock induces a cell response leading to profound changes in genome expression. Recently, N6-methyladenosine (m6A) RNA modification has been implicated in this response, but with limited information of its role in the heat-induced reprograming of gene expression. Most of m6A molecular and cellular functions rely on m6A readers and the best characterized m6A readers are members of the YTH-domain-containing protein family present from yeast to humans. To investigate the function of the nuclear m6A reader YTHDC1, we characterized its binding partners.

2023-01-11 | PXD037414 | Pride

Mitochondrial Fission 1 (FIS1) knockdown effect on the transcriptome of leukemia cell line MOLM-13 cells

Project description:To explore the function of Mitochondrial Fission 1 (FIS1) in acute myeloid leukemia (AML), we used shRNA to knock down the expression of FIS1 in leukemia cell line MOLM-13 cells and performed RNA-seq experiments to profile transcriptional changes upon FIS1 depletion.

2018-06-01 | GSE114111 | GEO

The effects of YTHDC1 on islet β-cell function

Project description:The goal of this study is to investigate how YTHDC1 regulates islet β-cell function. Our study represents the first detailed analysis of islet transcriptomes from Ythdc1flox/flox and Ythdc1-βKO mice, generated by RNA-seq technology. The RNA-seq analysis showed that 2869 genes were downregulated and 2825 genes were upregulated in the pancreatic islets of Ythdc1-βKO mice.

2022-10-19 | GSE209840 | GEO

YTHDC1-Hyper tribe uncover YTHDC1 binding sites in human leukemia cells

Project description:YTHDC1-Hyper tribe uncover YTHDC1 binding sites in human leukemia cells

| PRJNA708310 | ENA

Mitochondrial Fission 1 (FIS1) knockdown effect on the H3K27Ac status of leukemia cell line MOLM-13 cells

Project description:To examine if loss of FIS1 would alter the H3K27Ac status of leukemic cells, we used shRNA to knock down the expression of FIS1 in leukemic cell line MOLM-13 cells and performed H3K27Ac CHIP-seq to characterize any changes in the H3K27Ac marks upon loss of FIS1.

2018-06-01 | GSE114106 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data