NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM3473347 Query DataSets for GSM3473347
Status Public on Jun 23, 2020
Title WT H3K9ac_ChIPSeq
Sample type SRA
 
Source name alveolar macrophage
Organism Mus musculus
Characteristics strain: FVB/NJ backcross to C57BL/6 over 10 generations
tissue: lung
cell type: alveolar macrophage
age: 8-12 weeks
genotype: wild-type
chip antibody: H3K9ac (Epigentek, Cat. #A4022)
Extracted molecule genomic DNA
Extraction protocol The CD45+CD11c+SiglecF+ lung alverolar macrophages (AMs) were sorted by FACS Aria II flow cytometer. Cell pellets from the freshly isolated AMs were directly frozen at -80°C. The samples were then submitted to EpiGentek for ChIP, library preparation, and sequencing.
The cells were fixed with 1% formaldehyde and chromatin was isolated using ChromaFlashTM Chromatin Extraction Kit. Chromatin was sheared using the Episonic2000 Sonicatin System. ChIP was performed using an antibody against HDAC3, H3K27ac or H3K9ac on the chromatin and Input DNA (without immunoprecipitation) was used as background. After adapter linking, library was size-selected (100-300 bp) and PCR-amplified. Ten nanomolar of sample libraries were provided for next generation sequencing.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 4000
 
Data processing bcl2fastq v2.20.0.422 conversion software used for basecalling.
Raw ChIP-seq reads were quality checked using the software FastQC version v0.10.1 and processed using BBDuk (v36.19) and seqtk (v1.2-r94, https://github.com/lh3/seqtk) to trim the adapters and low-quality bases, respectively.
The trimmed reads were then aligned to the mouse mm10 genome sequence using Bowtie2 (v2.2.5) and only uniquely matching reads were retained.
Mapping results of each ChIP and the input sample were subjected to ChIP enriched peak calling using the MACS2 (v2.1.1.20160309).
Peak annotation was conducted using ChIPseeker.
Genome_build: mm10
Supplementary_files_format_and_content: Excel files include PeakID, chromosome, start and end site, strand, peak score, focus ratio/region size, annotation, detailed annotation, distance to TSS, nearest promoterID, Entrez ID, nearest Unigene, nearest Refseq, nearest Ensembl, gene name, gene alias, gene description, gene type, fold_enrichment, -LOG10(pvalue), -LOG10(qvalue) and pileup for each Sample.
Supplementary_files_format_and_content: bedGraph files
 
Submission date Nov 14, 2018
Last update date Jun 26, 2020
Contact name Qing-Sheng Mi
E-mail(s) qmi1@HFHS.ORG
Organization name Henry Ford Health System
Department Dermatology
Lab Immunology Program
Street address One Ford Place
City Detroit
State/province Michigan
ZIP/Postal code 48202
Country USA
 
Platform ID GPL21103
Series (2)
GSE122532 The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage [ChIP-Seq]
GSE122533 The epigenetic regulator Histone Deacetylase 3 regulates the ontogeny and maintenance of tissue-resident macrophage
Relations
BioSample SAMN10422836
SRA SRX5007213

Supplementary file Size Download File type/resource
GSM3473347_annot_W_K9_S34_peaks.xlsx 1.1 Mb (ftp)(http) XLSX
GSM3473347_macs2_W-K9_S34_FoldEnrich.bedgraph.gz 4.0 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