Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Ribosome profiling analysis (Ribo-seq) of DDX41-knockdown or CX5461-treated K562 leukemia cell-line.

PROVIDER: PRJDB15060 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	DRR428600.fastq.gz	Fastqsanger.gz
	DRR428601.fastq.gz	Fastqsanger.gz
	DRR428602.fastq.gz	Fastqsanger.gz
	DRR428603.fastq.gz	Fastqsanger.gz
	DRR428604.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Homo sapiens

Project description:RNA-seq analysis of DDX41-knockdown K562 cells

| PRJDB13700 | ENA

Homo sapiens strain:K562

Project description:CLIP-seq analysis of Myc-tagged DDX41 on K562 leukemia cell-line.

| PRJDB11668 | ENA

Ribosome profiling of the retrovirus murine leukemia virus

Project description:Ribosome profiling (Ribo-Seq) (maps positions of translating ribosomes on the transcriptome) and RNA-Seq (quantifies the transcriptome) analysis of Rattus norvegicus cells infected with Moloney Murine Leukemia Virus (Mo-MuLV).

2018-01-17 | E-MTAB-6231 | biostudies-arrayexpress

Inherited and somatic defects in DDX41 in myeloid neoplasms

Project description:Most cases of adult myeloid neoplasms are routinely assumed to be sporadic. Here, we describe an adult familial acute myeloid leukemia (AML) syndrome caused by germline mutations in the DEAD/H-Box helicase gene DDX41. DDX41 was also found to be affected by somatic mutations in sporadic cases of myeloid neoplasms as well as in a biallelic fashion in 50% of patients with germline DDX41 mutations. Moreover, corresponding deletions on 5q35.3 present in 6% of cases lead to haploinsufficient DDX41 expression. DDX41 lesions caused altered pre-mRNA splicing and RNA processing. DDX41 is exemplary of other RNA helicase genes also affected by somatic mutations, suggesting that they constitute a family of tumor suppressor genes. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples.

2015-04-01 | E-GEOD-66668 | biostudies-arrayexpress

Project description:Ribosome profiling (Ribo-seq)

| PRJNA899535 | ENA

Homo sapiens strain:K562

Project description:ChIP-seq analysis for RNA polymerase II distribution in DDX41-knockdown K562 cells

| PRJDB13680 | ENA

Ribosome profiling of Japanese encephalitis virus infected Neuro2a cells

Project description:Ribosome profiling (Ribo-Seq) and RNA-Seq analysis of mouse neuroblastoma (Neuro2a) cells infected with Japanese Encephalitis Virus (JEV) P20778 Vellore strain. At 18 h post infection (p.i.), infected cells were treated with either cycloheximide (translation elongation inhibitor) or in combination with harringtonine (translation initiation inhibitor). Ribo-Seq libraries were prepared using a broad range of fragment lengths (25 to 70 nucleotides) and deep sequenced. This allowed for estimation of ribosomal frameshifting efficiency and discovery of a novel upstream open reading frame (uORF) in JEV along with perturbations in ribosome-associated tRNA levels upon JEV infection.

2021-07-05 | E-MTAB-9352 | biostudies-arrayexpress

Homo sapiens

Project description:Leukemia study / K562 cell line

| PRJNA90947 | ENA

HyperTRIBE Analysis for DDX41 in human leukemia cells

Project description:In HyperTRIBE analysis, a hyperactive mutant of the catalytic domain of ADAR enzyme is fused to an RNA-binding protein of interest in order to identify RNAs that are bound by the protein interest through RNA-sequencing (Rahman et al Nat Protoc. 2018). By discovery of RNAs where adenosines have been edited to iosines, the RNAs that were bound by the protein of interest and then edited by ADAR are identified genome-wide. We conducted this analyis for DDX41, an RNA Helicase protein with multiple described cellular functions, including RNA splicing and innate immune sensing. Because DDX41 mutations have been discovered in leukemia patients, this analysis was conducted in the human lyeloid leukemia cell line THP-1.

2022-06-01 | GSE178892 | GEO

Genome-wide identification of the translation ability of the RNC-SRP complex [RIBO-seq]

Project description:Ribosome profiling (Ribo-seq) analysis to identify number of ribosome-protected reads from CBC-associated mRNAs or eIF4E-associated mRNAs encoding either a signal sequence or transmembrane domain (TMD)

2024-04-12 | GSE245550 | 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