Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: the 16S rDNA sequence

PROVIDER: PRJNA498798 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8116680.fastq.gz	Fastqsanger.gz
	SRR8116681.fastq.gz	Fastqsanger.gz
	SRR8116682.fastq.gz	Fastqsanger.gz
	SRR8116683.fastq.gz	Fastqsanger.gz
	SRR8116684.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 9

Similar Datasets

Project description:16s rDNA sequence

| PRJNA327028 | ENA

ena-DATASET-KULVIB-04-03-2016-10:53:34:991-129 - samples

Project description:Firs 1106 16S rDNA data for the Flemish Gut Flora Project

| EGAD00001001936 | EGA

16S rDNA (v3-v4 region) sequencing of the cecal bacteria in control (CTL) and chronic nonbacterial prostatitis (CNP) rats

Project description:Prostate of SD rats was injected with 0.1 ml 1% carrageenan to induce chronic nonbacterial prostatitis, and the control rats injected with sterile saline. Then, the cecal contents were collected for 16S rDNA sequencing.

2021-07-07 | GSE179639 | GEO

Genome-wide contacts of rDNA units detected by 4C procedure in human genome [old]

Project description:4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected downstream from EcoRI site at coordinate 30487 in rDNA sequence with Accession number U13369.1.

2019-12-03 | GSE121413 | GEO

Generation of Hematopoietic TF-rDNA Atlas in Human and Mouse

Project description:Over 2000 publicly accessible human and mouse ChIP-Seq datasets for about 250 Transcription Factors and chromatin complexes from various databases (ENCODE, GEO) were mapped to custom-made human and mouse genomes containing a reference rDNA sequence of the appropriate species (Genbank U13369.1 for human, BK000964.3 for mouse). The read mapping density across the rDNA sequence was then extracted and normalized to the median in that dataset. Unbiased clustering and analysis, followed by curation, was performed to identify high-confidence patterns of rDNA occupancy for numerous hematopoietic TFs and TF families at canonical TF motif sequences. ************************ Data processing steps: FASTQs were trimmed using Trimmomatic with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:30 Reads were mapped to customized genomes (containing additional rDNA sequence) using Bowtie2 using the following parameter: -X 2000 Read density across the rDNA sequence was extracted using igvtools ************************

2022-01-15 | GSE191272 | GEO

Cooperative binding of DNA sequence non-specific HMGbox Factor Ubf and TBP-TAF complex SL1 determines RNA Polymerase I promoter recognition in vivo and its dysfunction underlies the Ubf-E210K neuroregression syndrome

Project description:Transcription of the >200 rRNA genes (rDNA) by RNA Polymerase I (RPI) determines as much as 35% of total nuclear RNA synthesis and is a major determinant of cell growth implicated in a range of hypertrophic and developmental disorders. Activation of the rDNA involves the formation of an extended nucleosome free region (NFR) by the multi-HMGbox factor UBTF, which is also implicated with the RPI specific TBP-TAFI factor SL1 in preinitiation complex formation. However, neither factor alone displays significant DNA sequence binding specificity. Here we show that in cell cooperation between SL1 and the UBTF1 splice variant creates the sequence specificity required for promoter recognition. While both UBTF1 and UBTF2 splice variants bind throughout the rDNA NFR, only UBTF1 binds at the rDNA promoters. Conditional deletion of the Taf1b subunit of SL1 depleted UBTF1 from the rDNA promoters but not from elsewhere across the rDNA NFR. We show RPI promoters are particularly poor binding sites for UBTF and suggest an induced-fit model in which promoter-specific remodelling by UBTF1 creates high affinity sites for SL1 binding. A mouse model of the UBTF-E210K pediatric neurodegeneration syndrome suggests this mutation affects cooperativity of UBTF-SL1 promoter recruitment and further supports the induced-fit model.

2022-02-03 | E-MTAB-11385 | biostudies-arrayexpress

Genome-wide contacts of rDNA units detected by 4C procedure in human genome [old.hs]

Project description:4C procedure was used for analysis of genomic contacts of rDNA units in HEK 293T cells. The primers for 4C were selected downstream from EcoRI site at coordinate 30487 in rDNA sequence with Accession number U13369.1.

2019-12-05 | GSE121417 | GEO

soil metagenome

Project description:bacteria strain:16S rDNA | isolate:16S rDNA Raw sequence reads

| PRJNA301176 | ENA

Genome-wide contacts of rDNA units detected by 4C procedure in human genome [hESM01]

Project description:4C-rDNA procedure was used for analysis of genomic contacts of rDNA units in hESM01 cells. The primers for 4C were selected downstream from EcoRI site at coordinate 30487 in rDNA sequence with Accession number U13369.1.

2021-08-11 | GSE175909 | GEO

Characterization of the Bacterial Diversity of Drinking Water From 3 Parisian Treatment Plants Using Genomic Approaches

Project description:We characterized the bacterial diversity of chlorinated drinking water from three surface water treatment plants supplying the city of Paris, France. For this purpose, we used serial analysis of V6 ribosomal sequence tag (SARST-V6) to produce concatemers of PCR-amplified ribosomal sequence tags (RSTs) from the V6 hypervariable region of the 16S rRNA gene for sequence analysis. Using SARST-V6, we obtained bacterial profiles for each drinking water sample, demonstrating a strikingly high degree of biodiversity dominated by a large collection of low-abundance phylotypes. In all water samples, between 57.2-77.4% of the sequences obtained indicated bacteria belonging to the Proteobacteria phylum. Full-length 16S rDNA sequences were also generated for each sample, and comparison of the RSTs with these sequences confirmed the accurate assignment for several abundant bacterial phyla identified by SARST-V6 analysis, including members of unclassified bacteria, which account for 6.3-36.5% of all V6 sequences. These results suggest that these bacteria may correspond to a common group adapted to drinking water systems. The V6 primers used were subsequently evaluated with a computer algorithm to assess their hybridization efficiency. Potential errors associated with primer-template mismatches and their impacts on taxonomic group detection were investigated. The biodiversity present in all three drinking water samples suggests that the bacterial load of the drinking water leaving treatment plants may play an important role in determining the downstream community dynamics of water distribution networks. 3 different drinking water samples (Orly, Ivry, Joinville drinking water sample)

2009-01-07 | E-GEOD-14318 | biostudies-arrayexpress

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