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Series GSE102882 Query DataSets for GSE102882
Status Public on Aug 22, 2017
Title ChIP-seq Analysis of Estrogen Receptor-alpha on Treatment with Fulvestrant with internal and spike-in controls
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary A key challenge in quantitative ChIP-seq is the normalisation of data in the presence of genome-wide changes. Data-based methods often rely on assumptions that do not hold true. Misapplication of these methods to ChIP-seq data results in the suppression of the biological signal or erroneous measurement of differential occupancy. To develop methods that address this challenge, we generated three ChIP-seq datasets, each measuring Estrogen Receptor-alpha (ER) binding in MCF7 before and after 100 nm Fulvestrant treatment for 48 hours. The three methods were: a novel internal control using CTCF binding to normalise (SLX-14229 & SLX-14438); a spike-in control using H2av binding to D. Melanogaster chromatin (SLX-8047); and a spike-in control using the cross reactivity of ER antibody against M. Musculus chromatin (SLX-12998).
 
Overall design 3 ER ChIP-seq experiments implimenting internal or spike-in normalisation stratergies

Please note that there is no processed data for one dataset (SLX-12998) as these form part of a study to evaluate multiple methods and it is concluded at an early stage that this method isn't suitable, however the sequencing raw data is still relevant and provided for those who may be interested in re-evaluating the methods.
 
Contributor(s) Markowetz F, Holding AN
Citation(s) 29672735
Submission date Aug 21, 2017
Last update date May 15, 2019
Contact name Andrew Nicholas Holding
E-mail(s) andrew.holding@cruk.cam.ac.uk
Organization name University of Cambridge
Department CRUK Cambridge Institute
Street address Robinson Way
City Cambridge
ZIP/Postal code CB2 0RE
Country United Kingdom
 
Platforms (1)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (39)
GSM2747691 SLX-8047_1a_ER_Fulvestrant
GSM2747692 SLX-8047_1b_ER_none
GSM2747693 SLX-8047_2a_ER_Fulvestrant
Relations
BioProject PRJNA399154
SRA SRP115912

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE102882_CTCF_normalised_results.csv.gz 262.7 Kb (ftp)(http) CSV
GSE102882_H2av_normalised_results.csv.gz 153.9 Kb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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