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| Status |
Public on Jun 23, 2020 |
| Title |
WT H3K27ac_ChIPSeq |
| Sample type |
SRA |
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| Source name |
alveolar macrophage
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| 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: H3K27ac (Epigentek, Cat. #A4753)
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| 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
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| Submission date |
Nov 14, 2018 |
| Last update date |
Jun 26, 2020 |
| Contact name |
Qing-Sheng Mi |
| E-mail(s) |
qmi1@HFHS.ORG
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| Organization name |
Henry Ford Health System
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| Department |
Dermatology
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| Lab |
Immunology Program
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| Street address |
One Ford Place
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| City |
Detroit |
| State/province |
Michigan |
| ZIP/Postal code |
48202 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN10422838 |
| SRA |
SRX5007211 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3473345_annot_W_K27_S35_peaks.xlsx |
2.2 Mb |
(ftp)(http) |
XLSX |
| GSM3473345_macs2_W-K27_S35_FoldEnrich.bedgraph.gz |
4.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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