Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

IS-Seq: a novel bioinformatics pipeline for integration sites analysis

ABSTRACT: IS-Seq pipeline is developed,and 4 data sets are used to compare different abundance estimation methods of this pipeline

ORGANISM(S): Homo sapiens

PROVIDER: GSE203211 | GEO | 2023/08/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites.

Project description: Not available

| S-EPMC7606357 | biostudies-literature

A flexible Transcriptomic Analysis Pipeline (TAP) for quality control and functional assessment of transcriptomes

Project description:We developed a Transcriptomic Analysis Pipeline (TAP) as a flexible workflow for comprehensive transcriptome analysis from any species with a reference genome. We tested TAP in a case study to compare polyA+ and rRNA-depletion RNA-seq library protocols using Drosophila melanogaster following different thermal stress temperatures. TAP provides a flexible and complete pipeline to enable researchers to extract more biologically relevant interpretations by integrated and interactive transcriptome analysis.

2023-11-09 | GSE229448 | GEO

A new pipeline SPICE identifies novel JUN-IKZF1 composite elements

Project description:Transcription factor partners can cooperatively bind to DNA composite elements to augment gene transcription. Here, we report a novel protein-DNA binding screening pipeline, termed Spacing Preference Identification of Composite Elements (SPICE), that can systematically predict protein binding partners and DNA motif spacing preferences. SPICE de novo predicted known composite elements, including AP1-IRF composite elements (AICE) and STAT5 tetramers, and also predicted a range of novel binding partners, including JUN-IKZF1 composite elements. We confirmed cooperative binding of JUN and IKZF1 to an upstream conserved noncoding region, CNS9, in the human IL10 gene, that contains a non-canonical IKZF1 site, and the activity of an IL10-luciferase reporter construct depended on both this site and the AP1 binding site within this composite element in primary B and T cells. Our findings reveal an unappreciated global association of IKZF1 and AP1, and establish SPICE as a valuable new pipeline for predicting novel transcription binding complexes.

2023-11-05 | GSE230035 | GEO

RNA-seq dynamic transcriptomic pipeline

Project description:RNA-seq dynamic transcriptomic pipeline

| PRJNA524471 | ENA

VISPA2: a scalable pipeline for high-throughput identification and annotation of vector integration sites.

Project description: Not available

| S-EPMC5702242 | biostudies-literature

Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions using RNA-Seq Data

Project description:We developed a bioinformatics approach called the Read-Split-Walk (RSW) pipeline, and evaluated it using two Ire1? heterozygous and two Ire1?-null samples. The 26nt non-canonical splice site in Xbp1 was detected as the top hit by our RSW pipeline in heterozygous samples but not in the negative control Ire1? knockout samples. We compared the Xbp1 results from our approach with results using the alignment program BWA, STAR, Exonerate and the Unix “grep” command. We then applied our RSW pipeline to RNA-Seq data from the SKBR3 human breast cancer cell line. RSW reported a large number of non-canonical spliced regions for 108 genes in chromosome 17, which were identified by an independent study. Identification of non-canonical spliced regions for mouse MEF samples (two Ire1? heterozygous and two Ire1?-null samples)

2014-07-29 | E-GEOD-54631 | biostudies-arrayexpress

Novel Bioinformatics Method for Identification of Genome-Wide Non-Canonical Spliced Regions using RNA-Seq Data

Project description:We developed a bioinformatics approach called the Read-Split-Walk (RSW) pipeline, and evaluated it using two Ire1α heterozygous and two Ire1α-null samples. The 26nt non-canonical splice site in Xbp1 was detected as the top hit by our RSW pipeline in heterozygous samples but not in the negative control Ire1α knockout samples. We compared the Xbp1 results from our approach with results using the alignment program BWA, STAR, Exonerate and the Unix “grep” command. We then applied our RSW pipeline to RNA-Seq data from the SKBR3 human breast cancer cell line. RSW reported a large number of non-canonical spliced regions for 108 genes in chromosome 17, which were identified by an independent study.

2014-07-29 | GSE54631 | GEO

An analytical pipeline for identifying and mapping the integration sites of HIV and other retroviruses.

Project description: Not available

| S-EPMC7063773 | biostudies-literature

INSPIIRED: A Pipeline for Quantitative Analysis of Sites of New DNA Integration in Cellular Genomes.

Project description: Not available

| S-EPMC5363316 | biostudies-literature

SPOROS: A pipeline to analyze DISE/6mer Seed Toxicity

Project description:The SPOROS pipeline is a read-based sequence analysis pipeline for studying 6mer Seed Toxicity in mouse and human RNA-seq data.

2021-08-22 | GSE182222 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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