Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: J1-16S

PROVIDER: PRJNA849867 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19744794_1.fastq.gz	Fastqsanger.gz
	SRR19744794_2.fastq.gz	Fastqsanger.gz
	SRR19744795_1.fastq.gz	Fastqsanger.gz
	SRR19744795_2.fastq.gz	Fastqsanger.gz
	SRR19744796_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Mapping of internal monophosphate 5’ ends of Bacillus subtilis messenger RNAs and ribosomal RNAs in wild-type and ribonuclease-mutant strains

Project description:The narrow-specificity endoribonuclease RNase III and the 5’ exonuclease RNase J1 have been recently found to be not essential in the Gram-positive model organism, Bacillus subtilis. In this study, we performed a global analysis of internal 5’ ends that are generated or acted upon by these enzymes. An RNA-Seq protocol known as PARE (Parallel Analysis of RNA Ends) was used to capture 5’ monophosphorylated RNA ends in ribonuclease wild-type and mutant strains. Comparison of PARE peaks in strains with RNase III present or absent showed that, in addition to its well-known role in ribosomal (rRNA) processing, many coding sequences and intergenic regions were direct targets of RNase III. A set of regular RNA-seq experiments were performed to investigate RNA profiles in these strains and used to account for the changes in RNA abundance indirectly caused by the loss of RNase III in PARE. The PARE analysis also revealed an accumulation of 3’-proximal peaks that correlated with the absence of RNase J1, confirming the importance of RNase J1 in degrading RNA fragments that contain the transcription terminator structure. In addition, an endonuclease cleavage just two nucleotides downstream of the 16S rRNA 3’ end was discovered with PARE analysis. This latter observation begins to answer, at least for B. subtilis, a long-standing question on the exonucleolytic vs. endonucleolytic nature of 16S rRNA maturation

2016-01-27 | GSE77217 | GEO

Project description:J1 16S rRNA sequence

| PRJNA847756 | ENA

ChIP-seq of RNase J1 null strain

Project description:RNase J1 is the first nuclease with 5’-3’ exonuclease activity in bacteria and plays an important role in the maturation and degradation of mRNA. RNase J1 could also play a role in transcription termination of aberrant complexes. RNase J1 could bind to nascent RNA in such complexes, degrade the nascent RNA, and upon catching up with RNA polymerase (RNAP) dissociate the complex. Similar model was showed in eukaryotes. We did ChIP-seq to confirm our hypothesis.

2019-12-31 | E-MTAB-5659 | biostudies-arrayexpress

Comparison of Gene Expression Profiles of J1 ES and J1 EB Cells.

Project description:Comparison of gene expression profiles of J1 embryonic stem cells and J1 embryoid bodies. This study should reveal genes that, when expressed, are responsible for the maintenance of the stem cell phenotype. Keywords: other

2005-09-01 | GSE3223 | GEO

AICAR can modulate the expression of microRNA in J1 mESC

Project description:We have demonstrated AICAR can maintain J1 mouse ES cells pluripotency in our previous research, yet its effects on ES cells miRNAs expression remain a mystery. In this study, we performed small RNA (sRNA) High-throughput sequencing using Illumina HiSeq 2000 to investigate the influence of AICAR on J1 mouse ES cells miRNAs expression and further found the mechanism of how miRNAs affect ES cells pluripotency maintenance. Samples that treated by DMSO is used as a control.

2014-02-06 | GSE54586 | GEO

Establishment of ganglioside GD2-expressing extranodal NK/T-cell lymphoma cell line with scRNA-seq analysis

Project description:Extranodal natural killer (NK)/T-cell lymphoma, nasal type (ENKL), known for its poor prognosis and association with Epstein-Barr virus, has a new development with the establishment of the ENKL-J1 cell line. Derived from a patient's bone marrow, ENKL-J1 cells express the ganglioside GD2, making them targets for GD2-directed chimeric antigen receptor T cells. This discovery positions GD2 as a potential therapeutic target. Genetic analysis of ENKL-J1 revealed variants in TP53 and TET2. Single-cell RNA sequencing indicated high expression of genes in key oncogenic pathways such as JAK-STAT, NF-κB, and MAPK, along with genes linked to multidrug resistance, tumor suppression, and anti-apoptosis. In vitro, molecular targeting agents like eprenetapopt, tazemetostat, and vorinostat effectively induced apoptosis in these cells, with GD2-directed T cells also showing cytotoxicity in vivo. The ENKL-J1 cell line, therefore, provides valuable insights for developing treatments for ENKL, especially in advanced stages.

2023-12-23 | GSE251683 | GEO

Expression data in Srf KO and Srf WT murine muscle cells

Project description:The objective of the study is to caracherize the genes that are regulated by Srf in myoblasts at day 0 (J0) and in differentiated cells at day 1 (J1) and day 3 (J3). We used microarrays to investigate gene expression in Srf KO and Srf WT muscle cells at day 0 (J0), day 1 (J1) and day 3 (J3) of differentiation

2017-12-20 | GSE105125 | GEO

Genes plus and minus LIF

Project description:This study was undertaken in order to characterize the functions of Rex-1 and identify potential Rex-1 target genes.Both alleles of the Rex-1 gene were disrupted in J1 mouse embryonic stem cells. Gene expression levels in one of the resulting Rex-1 knockout cell lines was compared to that of J1 wild type cells. Keywords: cell type comparison

2009-03-17 | GSE9978 | GEO

Yersinia sp. J1 strain:J1

Project description:Yersinia sp. J1 strain:J1 Genome sequencing

| PRJNA1265709 | ENA

Project description:J1-Metagenomes

| PRJNA850074 | ENA