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Sample GSM3679106 Query DataSets for GSM3679106
Status Public on Jul 01, 2019
Title PTU_PV_rep2_PVexpH3K27Ac
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics tissue: liver
genotype: TRbetaPV
treatment: PTU
chip antibody: H3K27Ac (Abcam, ab4729)
Extracted molecule genomic DNA
Extraction protocol Crosslinked sonicated chromatin was IP'ed antibody and protein A/G agarose beads. DNA was extracted by phenol/choloroform.
ChIP-seq were constructed using the NEBNext Library prep kit according to manufacturer´s (NEB) instructions.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 1500
 
Data processing RNA-seq and ChIP-seq sequencing data was aligned to mm9 using STAR
Differential RNA expression, H3K27Ac and H3K9Ac were analysed by DESeq2
Bedgraph files were generated using HOMER
Nomilized tag counts were optained using HOMER
H3K27Ac and H3K9Ac domains were indentified using HOMER
Genome_build: mm9
Supplementary_files_format_and_content: Bedgraphs, peak bed file and text file with RPKM
 
Submission date Mar 19, 2019
Last update date Jul 02, 2019
Contact name Lars Grøntved
E-mail(s) larsgr@bmb.sdu.dk
Phone +45 24 60 14 06
Organization name University of Southern Denmark
Department Biochemistry and Molecular Biology
Street address Campusvej 55
City Odense
ZIP/Postal code 5230
Country Denmark
 
Platform ID GPL18480
Series (1)
GSE128535 Histone 3 K9 and K27 acetylation of enhancers in response to thyroid hormone
Relations
BioSample SAMN11166364
SRA SRX5543265

Supplementary file Size Download File type/resource
GSM3679106_H3K27Ac_PTU_PV_rep2_PVexp.bedgraph.gz 36.0 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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