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| Status |
Public on Jan 25, 2024 |
| Title |
RD-RD-AT-Macro1 |
| Sample type |
SRA |
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| Source name |
ATM-specific nuclei from HFD mice
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| Organism |
Mus musculus |
| Characteristics |
Stage: adult
gender: male
strain: C57Bl/6J
diet: RD-RD
cell type: adipose tissue macrophages
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| Growth protocol |
Adult male C57Bl/6J mice were fed a high-fat diet (HFD: 60% lipid content) for 11 weeks and then switched them to a regular diet (RD: 10% lipid content) for 9 weeks to trigger weight loss (HFD-RD mice). Control groups were fed a RD throughout the study (20 weeks; RD-RD mice) or a HFD throughout the study (11weeks; HFD mice).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
FACS-sorted ATMs were used for ATAC-seq and nuclei were isolated as previously described (Curr Protoc Mol Biol. 2016; 109: 21.29.1–21.29.9). Briefly, isolated cells were centrifuged at 500xg for 5 min at 4°C and then resuspended in ice-cold PBS+0.04% BSA. The cell lysis was performed for 5 minutes on ice by adding 45μl lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Nonidet P-40, 0.001% Digitonin, and 1% BSA). After lysis, 50μl ice-cold wash buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, and 1% BSA) were added and then centrifuged at 500 × g for 5 min at 4 °C. After one more wash, the washed nuclei were counted and used for the transposase reaction.
The library was constructed as cited previously (doi: 10.1002/0471142727.mb2129s109), using Nextera Tn5 Transposase from Illumina
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Reads were aligned to GRCm38 reference genome using Bowtie2.2.6
PCR duplicates were removed with Picard MarkDuplicates 2.4.1 and reads mapping to mitochondiral DNA were removed.
Deeptools was used to shift reads coordinates to represent the real Tn5 binding site and to remove ENCODE's blacklisted regions (signal artefact regions).
MACS 2.0.10 was used for peak calling using q-value < 0.001 to define peaks
DESeq2 was used to identify DARs (differentially accessible regions).
Genome_build: GRcm38
Supplementary_files_format_and_content: Differentially accessible regions identified by DESeq2
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| Submission date |
May 27, 2021 |
| Last update date |
Jan 25, 2024 |
| Contact name |
Mike Sapieha |
| E-mail(s) |
mike.sapieha@umontreal.ca
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| Organization name |
Hôpital Maisonneuve-Rosemont
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| Street address |
5415 Boul. L'Assomption
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| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H1T2M4 |
| Country |
Canada |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE175614 |
Global chromatin accessibility using an Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) reveals epigenomic reprogramming of Adipose tissue macrophages toward proinflammatory and proangiogenic phenotypes in formerly obese mice. |
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| Relations |
| BioSample |
SAMN19365283 |
| SRA |
SRX11003120 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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