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Sample GSM5357023 Query DataSets for GSM5357023
Status Public on Dec 22, 2021
Title H3k27me3-ko-2
Sample type SRA
 
Source name Alveolar macrophage
Organism Mus musculus
Characteristics background strain: C57BL/6
tissue: Lung
cell type: Alveolar macrophage
transgenic mouse genotype: Suz12 cKO
primary antibody: anti-H3K27me3 Abcam
Extracted molecule genomic DNA
Extraction protocol Alveolar macrophages sorted from the lung of wt or Suz12cKO mouse were bound to concanavalin A cated magnetic beads (Bags laboratories) and were subjected for immunoprecipitation with 1ul (0.5μg) of primary antibody (anti-H3K27me3 Abcam)
Hyperactive in situ ChIP Library Prep Kit was purchased from Vazyme and libraries were generated following manufacturer recommendations.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description H3k27me3-ko-2_S4
Data processing Library strategy: Cut&Tag
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the mouse genome using the align function of RSubread 2.2.6.
Read counts were summarized by Entrez Gene ID using the featureCounts function of Rsubread 2.6.1 and Rsubread's built-in NCBI annotation. The supplementary file GenewiseCounts.tsv.gz provides the gene-level counts for all the samples.
Genome_build: mm10 (NCBI build 38.1)
Supplementary_files_format_and_content: Tab-delimited text files; columns represent Entrez Gene ID, total gene length and the number of reads mapping to that gene and their promoter region (trimmed at 3000bp upstream).
 
Submission date Jun 04, 2021
Last update date Dec 22, 2021
Contact name Gordon K Smyth
E-mail(s) smyth@wehi.edu.au
Phone (+61 3) 9345 2326
Fax (+61 3) 9347 0852
URL http://www.wehi.edu.au
Organization name Walter and Eliza Hall Institute of Medical Research
Department Bioinformatics
Lab Smyth
Street address 1G Royal Pde
City Parkville
State/province Vic
ZIP/Postal code 3052
Country Australia
 
Platform ID GPL19057
Series (2)
GSE176117 RNA-seq profiling of bone marrow-derived alveolar macrophages, foetal-derived alveolar macrophages and foetal-derived Langerhans cells from the lungs of wildtype and Suz12 knockout mice
GSE176148 H3K27me3 Cut&Tag profiling of bone marrow-derived alveolar macrophages from wildtype and Suz12 knockout mice
Relations
BioSample SAMN19570080
SRA SRX11067320

Supplementary file Size Download File type/resource
GSM5357023_H3k27me3-ko-2_S4.tsv.gz 186.2 Kb (ftp)(http) TSV
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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