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Series GSE70482 Query DataSets for GSE70482
Status Public on Aug 17, 2015
Title ChIPmentation: fast, cheap, low-input ChIP-seq for histones and transcription factors
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Chromatin immunoprecipitation followed by next generation sequencing (ChIP-seq) is widely used to map histone marks and transcription factor binding throughout the genome. Here we present ChIPmentation, a method that combines ChIP with sequencing library preparation by Tn5 transposase (“tagmentation”). ChIPmentation introduces sequencing-compatible adapters in a single-step reaction directly on bead-bound chromatin, which reduces time, cost, and input requirements, making ChIPmentation a convenient and high-throughput alternative to existing ChIP-seq protocols.
 
Overall design This submission includes sequencing data for 87 samples: 52 ChIPmentation and 24 ChIP-seq for 10 different antibodies with at least two biological replicates each and matched immunoglobulin controls in the majority of cases; 2 ATAC-seq samples were sequenced for comparison; Additionally, 9 samples of a experimental protocol which we called “ChIP-tagmentation” were produced without replication.
 
Contributor(s) Schmidl C, Rendeiro AF, Sheffield NC, Bock C
Citation(s) 26280331
Submission date Jul 02, 2015
Last update date Mar 20, 2019
Contact name Christoph Bock
E-mail cbock@cemm.oeaw.ac.at
Organization name CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences
Street address Lazarettgasse 14
City Vienna
ZIP/Postal code 1090
Country Austria
 
Platforms (2)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (87)
GSM1782687 ChIPmentation of 100 thousand K562 cells with CTCF antibody - replicate 1
GSM1782688 ChIPmentation of 100 thousand K562 cells with CTCF antibody - replicate 2
GSM1782689 ChIPmentation of 100 thousand K562 cells with GATA1 antibody - replicate 1
Relations
BioProject PRJNA288801
SRA SRP060245

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
GSE70482_RAW.tar 14.6 Gb (http)(custom) TAR (of BIGWIG)
Raw data are available in SRA
Processed data provided as supplementary file

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