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| 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
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| 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.
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| 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).
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| 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 |
| E-mail(s) |
gergana.bounova@unil.ch, Nouria.Hernandez@unil.ch
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| Organization name |
University of Lausanne
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| Department |
Center for Integrative Genomics
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| Lab |
Hernandez
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| Street address |
Quartier Sorge, bâtiment Génopode
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| City |
Lausanne |
| State/province |
VD |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA226591 |
| SRA |
SRP032521 |
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