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Series GSE115822 Query DataSets for GSE115822
Status Public on Jun 15, 2018
Title PIXUL-ChIP-seq analysis of genome-wide epigenetic marks binding in human HCT116 cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary High throughput PIXUL-ChIP-seq genome-wide study allows the mapping of epigenetic marks in human HCT116 cells.
 
Overall design Human HCT116 cells were grown and sheared in a 96-well plate using PIXUL, high throughput chromatin sonication instrument. HCT116 cells were grown to a density of 200,000 cells per well, crosslinked, quenched, and sonicated for 6 minutes per well in 100µL on the PIXUL 96-well sonicator. ChIP and library prep was performed for each factor from a single well using Active Motif’s Low Cell ChIP-Seq Kit (Catalog number 53084). Libraries were sequenced on a NextSeq 500 as SE75 with dual 8bp indexing, allowing for PCR de-duplication with molecular identifiers at the i5 position (see product manual).
 
Contributor(s) Bomsztyk K, Blattler A, Mar D, Matula T, Wang Y
Citation(s) 30927002
NIH grant(s)
Grant ID Grant title Affiliation Name
R01 DK103849 Transcriptional and epigenetic control of angiogenic genes in sepsis-induced acute kidney injury. UNIVERSITY OF WASHINGTON KAROL BOMSZTYK
R21 GM111439 Integrated microplate platform for epigenetic analysis UNIVERSITY OF WASHINGTON KAROL BOMSZTYK
R33 CA191135 Next generation technology to detect epigenetic alterations in human tissues UNIVERSITY OF WASHINGTON KAROL BOMSZTYK
Submission date Jun 14, 2018
Last update date Apr 04, 2019
Contact name Karol Bomsztyk
E-mail(s) karolb@u.washington.edu
Phone 206-616-7949
Organization name University of Washington
Department Medicine
Street address 850 Republican Street
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (7)
GSM3190501 H3K4me1-ChIP-seq
GSM3190502 H3K4me3-ChIP-seq
GSM3190503 H3K9Ac-ChIP-seq
Relations
BioProject PRJNA476139
SRA SRP150549

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Supplementary file Size Download File type/resource
GSE115822_RAW.tar 672.7 Mb (http)(custom) TAR (of BROADPEAK, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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