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Series GSE52049 Query DataSets for GSE52049
Status Public on Apr 02, 2014
Title Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization.
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Purpose: Description of a spike-adjusting-method (SAM) to normalize ChIP-seq data .
Methods: We performed ChIP-seq of POLR3D and POLR2B with mouse liver supplemented with 2.5% of human DNA. Human DNA will be used as an internal control for ChIP-seq quantification.
Results: We show that using the SAM for ChIP-seq quantification improve similarity of POLR3D and POLR2B ChIP-seq replicates samples and improve difference between samples originate from different conditions.
Conclusions: The SAM improves comparison of ChIP-seq samples, either by increasing similarity between replicates or by emphasise differences between conditions.
Overall design Chromatin Immuno-precipitations were performed with antibodies directed against POLR3D (Pol III) and POLR2B (Pol II) using mouse liver material supplemented with human DNA. Immuno-precipitated DNA was next sequenced using Illumina HiSeq. Three different concentrations of human spiked DNA were tested for the Pol III ChIP (2.5%, 5% and 10%). We also sequenced the corresponding inputs (crosslinked DNA from mouse liver). Two concentrations of human spiked DNA (5% and 10%) were tested for the Pol 2 ChIP. We also sequenced the corresponding inputs (crosslinked DNA from mouse liver).
Contributor(s) Bonhoure N, Bounova G, Bernasconi D, Praz V, Lammers F, Canella D, Willis IM, Herr W, Hernandez N, Delorenzi M
Citation(s) 24709819
Submission date Nov 04, 2013
Last update date May 15, 2019
Contact name Gergana Bounova
Organization name University of Lausanne
Department Center for Integrative Genomics
Lab Hernandez
Street address Quartier Sorge, bâtiment Génopode
City Lausanne
State/province VD
ZIP/Postal code 1015
Country Switzerland
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (10)
GSM1257991 97.5_R1
GSM1257992 95_R1
GSM1257993 90_R1
BioProject PRJNA226591
SRA SRP032521

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Supplementary file Size Download File type/resource
GSE52049_RAW.tar 860.0 Kb (http)(custom) TAR (of CSV)
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Raw data are available in SRA
Processed data provided as supplementary file

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