Experiment 'ChIP-seq Example Experiment'

Permalink:

http://www.geneprof.org/GeneProf/show?id=gpXP_000120

Name:

ChIP-seq Example Experiment

SRA Project ID:

N/A

Experiment Type:

Primary. This experiment presents primary research data. The analysis in this experiment is the data creators' original work.

Tags:

ChIP-seq example

Description:

This is an example experiment demonstrating the use of the ChIP-seq analysis wizard to quickly create and run an analysis pipeline that parses sequence reads from FASTQ formatted files, performs a quality control step, aligns the quality-controlled reads to the genome and looks for genomic regions with enriched binding for ChIP'ed protein.

Platform(s):

Illumina Genome Analyzer

Citation(s):

N/A

External URL(s):

ChIP-seq Analysis Tutorial:

http://www.geneprof.org/GeneProf/help_tutorials.jsp#tutorial:DiscoveringTranscriptionFactorBindingSites(ChIP-seq)

Reference Dataset(s):

Ensembl 58 Mouse Genes, NCBIM37 Assembly

Owner:

Halbritter F

Status:

Date Created:

11-Mar-2011

Last Modified:

14-Mar-2011 (show history?)

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Some things you might want to do with these data..

Batch export genome browser tracks (for UCSC, Ensembl, IGV, ..).
Inspect aligned reads, coverage and the like in the simple, in-built genome browser.
Export a PDF report for this experiment. The report describes the experimental analysis workflow and the main input and output datasets.

Input Data

ID (click for details)	Name	Source
gpDS_pub_mm_ens58_ncbim37	Ensembl 58 Mouse Genes, NCBIM37 Assembly	Import from Public Repository
gpDS_11_120_4_1	A	Upload
gpDS_11_120_5_1	B	Upload
gpDS_11_120_6_1	Control	Upload

Sample Groups and Experimental Factors

Associated Input(s)	Gene	Label	Organism	Platform	Sample Group
gpDS_11_120_4_1 : A	Dem1	A	Mus musculus	Illumina Genome Analyzer	A
gpDS_11_120_5_1 : B	Edem1	B	Mus musculus	Illumina Genome Analyzer	B
gpDS_11_120_6_1 : Control		Control	Mus musculus	Illumina Genome Analyzer	Control

Main Experimental Results

This is a selection of main results from the data analysis in this experiment. All intermediate results and more data are available from the workflow designer.

Sequence Data Statistics after Quality Control
Read Alignment Statistics
DNA-Protein Binding Peaks
TFBS Statistics
Regulated Genes
TFAS
Regulated Genes (narrow window)
Sequence Data Statistics before Quality Control

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Analysis Workflow

This is a simplified schematic representation of the analysis workflow used in this experiment. For more details use the fully-featured workflow designer.

Workflow Designer

Colours represent types of data (sequences, genomic regions, features, references and files.

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