Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Xdrop - Oxford Nanopore long read sequencing of HAP1 and HepG2 tRNA gene deletion clones

ABSTRACT: Xdrop - Oxford Nanopore long read sequencing of HAP1 and HepG2 tRNA gene deletion clones

PROVIDER: PRJEB46001 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR6150248.fastq.gz	Fastqsanger.gz
	ERR6150249.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Xdrop - Oxford Nanopore long read seqeuncing of HAP1 and HepG2 tRNA gene deletion clones

Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion clones in HAP1 (t72) and HepG2 (t15). By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.

2022-09-16 | E-MTAB-10652 | biostudies-arrayexpress

Xdrop - Oxford Nanopore long read seqeuncing of HepG2 genetic modified clones

Project description:This dataset contains Xdrop followed by oxford nanopore long read sequencing performed in target tRNA gene deletion (t8) and intergenic region deletion (i50) clones in HepG2 . By applying de novo assembly based approach to Xdrop-LRS data, we identified Cas9-induced on-target genomic alteration.

2022-09-16 | E-MTAB-11327 | biostudies-arrayexpress

ChIP-seq of Pol III and H3K4me3 in HAP1 and HepG2 tRNA gene deletion clones and control clones

Project description:This dataset contains ChIP-seq data of H3K4me3 and Pol III in single cell-derived control and CRISPR/Cas9 induced tRNA gene deletion clones in human cancer cell lines HAP1 and HepG2. In this study, we looked into functional Cas9-induced on-target genomic alteration in our tRNA gene deletion clones, HAP1 t72 and HepG2 t15.

2022-09-16 | E-MTAB-10651 | biostudies-arrayexpress

Xdrop - Oxford Nanopore long read seqeuncing of HepG2 genetic modified clones

Project description:Xdrop - Oxford Nanopore long read seqeuncing of HepG2 genetic modified clones

| PRJEB50072 | ENA

Generation of full-length circRNA libraries for Oxford Nanopore long-read sequencing

Project description:Preparation of libraries for circular RNA sequencing with Oxford Nanopore long-read sequencing

2022-08-09 | GSE197872 | GEO

Nanopore RNA-seq of polyA+ RNA from HAP1 and HEK293 cell lines

Project description:Sequencing was performed to assess the ability of Nanopore direct cDNA and native RNA sequencing to characterise human transcriptomes. Total RNA was extracted from either HAP1 or HEK293 cells, and the polyA+ fraction isolated using oligodT dynabeads. Libraries were prepared using Oxford Nanopore Technologies (ONT) kits according to manufacturers instructions. Samples were then sequenced on ONT R9.4 flow cells to generate fast5 raw reads in the ONT MinKNOW software. Fast5 reads were then base-called using the ONT Albacore software to generate Fastq reads.

2019-03-14 | E-MTAB-7778 | biostudies-arrayexpress

RNA-seq in HAP1 tRNA gene locus deleted clones and control clones

Project description:This dataset contains ploy-A tailed enriched RNA-seq data obtained from single cell-derived control and CRISPR/Cas9 induced tRNA gene deletion clones in the human cancer cell line HAP1. In this study, we found a large genomic deletion of the 10q23 locus in our Cas9 modified clones and further investigate the effect on the transcriptome.

2023-10-24 | E-MTAB-11858 | biostudies-arrayexpress

scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing [DataSet1: scNanoATAC-seq]

Project description:We present scNanoATAC-seq (Single-cell Assay for Transposase Accessible Chromatin by Oxford Nanopore Technologies Sequencing), an effective method for simultaneous detection of chromatin accessibility and genetic variation. Long fragments (about 4-5Kb) of single-cell ATAC-seq library were enriched and sequenced by Oxford Nanopore Technologies platform. Ends of long ATAC-seq fragments are regarded as chromatin accessibility signal in downstream analysis.

2022-09-07 | GSE194022 | GEO

scNanoATAC-seq: Long-read Single-cell ATAC-seq by Oxford Nanopore Technologies Sequencing [DATASet2: bulkATAC-seq]

2022-09-07 | GSE194023 | GEO

ChIP-seq of H3K27ac and H3K4me3 in HAP1 tRNA gene locus modified clones and control clones

Project description:This dataset contains ChIP-seq data profiling genomic binding of H3K27ac and H3K4me3 in single cell-derived control, as well as CRISPR/Cas9 induced tRNA gene deletion clones and intergenic region deletion clones in human cancer cell lines HAP1. In this study, we found a large genomic deletion of 10q23 in Cas9 modified clones and further investigate the effect of H3K27ac binding.

2023-10-24 | E-MTAB-11859 | 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