NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4090283 Query DataSets for GSM4090283
Status Public on Sep 23, 2019
Title PTU_WT_H3K4me1_rep2
Sample type SRA
 
Source name liver
Organism Mus musculus
Characteristics tissue: liver
genotype: WT
treatment: PTU
chip antibody: H3K4me1 (Abcam, ab8895)
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 NovaSeq 6000
 
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 Sep 23, 2019
Last update date Sep 24, 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 GPL24247
Series (1)
GSE128535 Histone 3 K9 and K27 acetylation of enhancers in response to thyroid hormone
Relations
BioSample SAMN12821260
SRA SRX6889466

Supplementary file Size Download File type/resource
GSM4090283_H3K4m1_PTU_WT_rep2.bedgraph.gz 30.4 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap