|
| Status |
Public on Dec 22, 2021 |
| Title |
H3k27me3-WT-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: Wild type
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-WT-2_S2
|
| 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 |
SAMN19570082 |
| SRA |
SRX11067322 |
