Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: HepG2 cell line Aristolochic Acid I exposure

PROVIDER: PRJNA1262723 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR33558055_1.fastq.gz	Fastqsanger.gz
	SRR33558055_2.fastq.gz	Fastqsanger.gz
	SRR33558056_1.fastq.gz	Fastqsanger.gz
	SRR33558056_2.fastq.gz	Fastqsanger.gz
	SRR33558057_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

4279c1dd-11f0-4345-aa4b-0102aaa1bc8f - samples

Project description:A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome - cell line data

| EGAD00001008963 | EGA

Single cell RNA-Seq of I2A rhabdoid cell line

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of I2A cell line Examination of gene expression in I2A rhabdoid cell line, as a negative control

2020-02-14 | GSE130021 | GEO

Difference of GATA4 and beta-catenin pulldown chromatin immunoprecipitated DNA in HePG2i cells line with and without DOX induced GATA4 expression

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of HePG2i cell line with and without DOX induced GATA4 expression by obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA.

2019-08-13 | GSE135714 | GEO

Single cell RNA-Seq of Neuroblastoma cell line (CLB-berlud)

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of Neuroblastoma cell line (CLB-berlud) Examination of gene expression in Neuroblastoma cell line (CLB-berlud), as a negative control

2020-02-14 | GSE130022 | GEO

Single-cell RNA sequencing of the CFS414 zebra finch cell line

Project description:The zebra finch is one of the most commonly studied songbirds in biology, particularly in genomics, neuroscience and vocal communication. However, this species lacks a robust cell line for molecular biology research and reagent optimization. We generated a cell line from zebra finch embryonic fibroblasts using the SV40 large and small T antigens, designated CFS414. This cell line demonstrates an improvement over previous songbird cell lines through continuous and density-independent growth, allowing for indefinite culture and monoclonal line derivation. Cytogenetic, genomic, and transcriptomic profiling established the provenance of this cell line and identified the expression of genes relevant to ongoing songbird research. This single-cell RNA sequencing experiment provided information on the gene expression landscape of the cell line, informing on its cell type, transcriptomic stability, and value to researchers utilizing the zebra finch as a model organism.

2022-02-04 | GSE195934 | GEO

P. pacificus PacBio genome sequencing

Project description:Single-molecule sequencing of the nematode model Pristionchus pacificus

| PRJEB20850 | ENA

The Methylomes of Six Bacteria

Project description:Six bacterial genomes, Geobacter metallireducens GS-15, Chromohalobacter salexigens, Vibrio breoganii 1C-10, Bacillus cereus ATCC 10987, Campylobacter jejuni subsp. jejuni 81-176 and Campylobacter jejuni NCTC 11168, all of which had previously been sequenced using other platforms were re-sequenced using single-molecule, real-time (SMRT) sequencing specifically to analyze their methylomes. In every case a number of new N6-methyladenine (m6A) and N4-methylcytosine (m4C) methylation patterns were discovered and the DNA methyltransferases (MTases) responsible for those methylation patterns were assigned. In 15 cases it was possible to match MTase genes with MTase recognition sequences without further sub-cloning. Two Type I restriction systems required sub-cloning to differentiate their recognition sequences, while four MTases genes that were not expressed in the native organism were sub-cloned to test for viability and recognition sequences. No attempt was made to detect 5-methylcytosine (m5C) recognition motifs from the SMRT sequencing data because this modification produces weaker signals using current methods. However, all predicted m6A and m4C MTases were detected unambiguously. This study shows that the addition of SMRT sequencing to traditional sequencing approaches gives a wealth of useful functional information about a genome showing not only which MTase genes are active, but also revealing their recognition sequences. Examination of the methylomes of six different strains of bacteria using kinetic data from single-molecule, real-time (SMRT) sequencing on the PacBio RS.

2012-10-04 | E-GEOD-40133 | biostudies-arrayexpress

Genome-wide mapping of nucleosome positioning and DNA methylation within Individual DNA molecules

Project description:DNA methylation and nucleosome positioning work together to generate chromatin structures that regulate gene expression. Nucleosomes are typically mapped using nuclease digestion requiring significant amounts of material and varying enzyme concentrations. We have developed a method (NOMe-seq) that uses a GpC methyltransferase (M.CviPI) and next generation sequencing to generate a high resolution footprint of nucleosome positioning genome-wide using less than 1 million cells while retaining endogenous DNA methylation information from the same DNA strand. Using a novel bioinformatics pipeline we show a striking anti-correlation between nucleosome occupancy and DNA methylation at CTCF regions, that is not present at promoters. We further show that the extent of nucleosome depletion at promoters is directly correlated to expression level and can accommodate multiple nucleosomes and provide genome-wide evidence that expressed non-CpG island promoters are nucleosome depleted. Importantly, NOMe-seq obtains DNA methylation and nucleosome positioning information from the same DNA molecule, giving the first genome-wide DNA methylation and nucleosome positioning correlation at the single molecule and thus, single cell level that can be used to monitor disease progression and response to therapy. Nucleosome Occupancy and Methylome-Sequencing (NOMe-Seq) on IMR90 cell line and 2 GBM cell lines

2012-09-12 | E-GEOD-40770 | biostudies-arrayexpress

Chromatin Profiling by Directly Sequencing Small Quantities of Immunoprecipitated DNA

Project description:Chromatin structure and transcription factor localization can be assayed genome-wide by sequencing genomic DNA fractionated by protein occupancy or other properties. However, current technologies involve multiple steps that introduce bias and inefficiency. Here we apply a single-molecule approach to directly sequence chromatin immunoprecipitated DNA with minimal sample manipulation. This method is accurate, compatible with just 50 picograms of DNA and should thus facilitate charting chromatin maps from limited cell populations. Application of a single-molecule approach to directly sequence chromatin immunoprecipitated DNA of the CTCF DNA binding protein.

2009-11-29 | E-GEOD-18699 | biostudies-arrayexpress

Methylome sequencing of Burkholderia pseudomallei strains Bp33 and Bp35

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of DNA methylations in Burkholderia pseudomallei. SMRTbell™ sequencing

2014-09-15 | E-GEOD-55168 | 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