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Series GSE64504 Query DataSets for GSE64504
Status Public on Jun 01, 2015
Title Multiplexing of ChIP-seq samples for a model experimental condition has minimal impact on peak detection
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary ChIP-seq experiments are standard experimental procedure for interrogating epigenetic states and protein-DNA interactions. Sequencing experiments are often designed according to the trade-off between the need to obtain maximum sequencing coverage limited funds. Multiplexing samples is a common approach to minimize cost and maximize information yield. We therefore performed an extensive ChiP-seq multiplexing study to gain a better understanding of the effect of multiplexing on the resulting peak detection and genomic annotation and to provide solid guidelines for multiplexing ChIP-seq studies. For a well characterized antibody, our results indicate that multiplexing to ~20M reads (roughly 8 samples per sequencing lane) is sufficient to capture most of the biological signal.
Multiplexing samples in sequencing experiments is a common approach to maximize information yield while minimizing cost. In most cases the number of samples that are multiplexed is determined by financial consideration or experimental convenience with limited understanding on the effects on the experimental results. Here we set to examine the impact of multiplexing ChIP-seq experiments on the ability to identify a specific epigenetic modification. We performed an analysis of peak detection to determine the effects of multiplexing. These include false discovery rates, size, position and statistical significance of peak detection and changes in gene annotation. We found that, for histone marker H3K4me3, one can multiplex up to 8 samples (7 IP + 1 input) at ~21 million reads each and still detect over 90% of all peaks found when using a full lane for sample. Furthermore, there are no variations introduced by indexing or lane batch effects and importantly there is no significant reduction in the number of genes with neighboring H3K4me3 peaks. We conclude that, for a well characterized antibody and therefore, model IP condition, multiplexing 8 samples per lane is sufficient to capture most of the biological signal.
Overall design We devised a multiplexing titration scheme starting from one full lane of ChIP and one lane of input samples down to 7 IP samples and one input in a single lane (Figure 1). The remainder of the flow cell contained two lanes of two ChIPs and two inputs, one lane of 5 ChIPs and one input, and one lane of 7 ChIPs and one input.
Contributor(s) Kacmarczyk TJ, Bourque C, Zhang X, Jiang Y, Houvras Y, Alonso A, Betel D
Citation(s) 26066343
Submission date Dec 24, 2014
Last update date May 15, 2019
Contact name Thadeous James Kacmarczyk
Organization name Weill Cornell Medicine
Department Medicine/Hematology-Oncology
Lab Epigenomics Core
Street address 1300 York Ave
City new york
State/province ny
ZIP/Postal code 10065
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (24)
GSM1572766 Sample_Input_Index_2_lane1
GSM1572767 Sample_H3K4me3_Index_2_lane2
GSM1572768 Sample_Input_Index_4_lane3
BioProject PRJNA271137
SRA SRP051534

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Supplementary file Size Download File type/resource
GSE64504_Targets_lane12.tar.gz 512.0 Kb (ftp)(http) TAR
GSE64504_Targets_lane3.tar.gz 2.8 Mb (ftp)(http) TAR
GSE64504_Targets_lane34.tar.gz 5.7 Mb (ftp)(http) TAR
GSE64504_Targets_lane4.tar.gz 2.9 Mb (ftp)(http) TAR
GSE64504_Targets_lane5.tar.gz 2.3 Mb (ftp)(http) TAR
GSE64504_Targets_lane6.tar.gz 3.1 Mb (ftp)(http) TAR
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