GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5029377 Query DataSets for GSM5029377
Status Public on May 11, 2021
Title TAC-Fat 60 (HiFat)-H3K9Bu
Sample type SRA
Source name heart tissue
Organism Mus musculus
Characteristics strain and age: C57/Bl/6J - 12 wk-old
diet: 60% Fat
Sex: male
surgical procedure: transverse aortic constriction (TAC)
antibody: H3K9Bu
Extracted molecule genomic DNA
Extraction protocol Nuclei were extracted from heart tissue, sonicated, and histone-DNA complexes were precipitated with anti-H3K9Bu or anti-H3K9ac (a pool of 3, each)
Library was constructed by Active Motif (
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing The 75-nt single-end (SE75 sequence reads generated by Illumina sequencing (using NextSeq 500) are mapped to the genome using the BWA algorithm (“bwa aln/samse” with default settings)
Only reads that pass Illumina’s purity filter, align with no more than 2 mismatches, and map uniquely to the genome are used in the subsequent analysis. In addition, duplicate reads (“PCR duplicates”) are removed.
Since the 5´-ends of the aligned reads (= “tags”) represent the end of ChIP/IP-fragments, the tags are extended in silico (using Active Motif software) at their 3´- ends to a length of 200 bp, which corresponds to the average fragment length in the size-selected library. To identify the density of fragments (extended tags) along the genome, the genome is divided into 32-nt bins and the number of fragments in each bin is determined. This information (“signal map”; histogram of fragment densities) is stored in a bigWig file, which can be visualized in genome browsers (see Section VI.). bigWig files also provide the peak metrics in the Active Motif analysis program described below.
Peak finding was performed using SICER (Zang et al., Bioinformatics 25, 1952-1958, 2009).
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files - Binary files that can be opened in or uploaded to genome browsers and show the fragment density for 32-nt bins along the genome (“signal map”).
Supplementary_files_format_and_content: MERGED (PEAK) REGIONS – an 'excel' file comparing peak region metrics between different samples
Submission date Jan 21, 2021
Last update date May 11, 2021
Contact name Maha Abdellatif
Phone 9739721254
Organization name Rutgers-University
Department Cell Biology and Molecular Medicine
Street address 185 S. Orange Ave.
City Newark
State/province NJ
ZIP/Postal code 07103
Country USA
Platform ID GPL19057
Series (1)
GSE165279 The effect of diet on H3K9-butyryl and H3K9-acetyl in the heart before and after transverse aortic constriction in C57Bl/6J mice
BioSample SAMN17487021
SRA SRX9912234

Supplementary file Size Download File type/resource 129.7 Mb (ftp)(http) BW
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