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| Status |
Public on Sep 29, 2023 |
| Title |
WT, rep1 (ApoE KO) |
| Sample type |
SRA |
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| Source name |
Bone marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: Bone marrow
cell line: Primary
cell type: BMDM
genotype: Baf60af/f, Lyz2 Cre-, ApoE KO
treatment: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cryopreserved BMDM were sent to CD Genomics for ATAC-Seq nuclei preparation following internal QC and nuclei prep propotocl in the company.
The libraries were constructed using Nextera DNA perp kit, followed byquantitation with the Qubit 2.0 DNA HS Assay kit, and quality assessment on a TapeStation HS D1000 kit. The libraries were pooled and sent for PE-150 sequencing on a shared flowcell on the NovaSeq6000.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
150PE
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| Data processing |
We use FastQC(FastQC)(v0.11.8) to assess the overall quality of each sequenced sample.
We use TrimGalore(TrimGalore)(v0.4.5) and cutadapt(Martin)(v1.15) with the following parameters: –nextera -e 0.1 –stringency 6 –length 20 –nextseq 20.
We align trimmed reads to mm10 with Bowtie2(Langmead and Salzberg, 2012)(v2.3.4.1) with the following parameters: -X 2000 –no-mixed –no-discordant, and defaults multi-seed length of 20bp with 0 mismatches.
Alignments to autosomes are kept (i.e.sex chromosomes and mitochondrial alignments are removed), duplicates marked by Picard are removed, and alignments below a MAPQ threshold are removed. These filtering steps are performed with samtools(Liet al., 2009)(v1.2) and the parameters: -q 10 -F 1024.
Reads completely overlapping blacklisted regions(ENCODE Blacklist Regions)are removed with bedtools(Quinlan and Hall, 2010)(v2.28.0).
Sample-wise peaks are called with macs2 with flags: -f BAMPE –nomodel –shift -100 –extsize 200 –gsize mm.
Assembly: mm10
Supplementary files format and content: bed(peak)
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| Submission date |
Jul 28, 2023 |
| Last update date |
Sep 29, 2023 |
| Contact name |
Yang Zhao |
| E-mail(s) |
ypharan@umich.edu
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| Organization name |
University of Michigan
|
| Street address |
2800 Plymouth Rd
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| City |
Ann Arbor |
| ZIP/Postal code |
48105 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE224667 |
Genome-wide maps of chromatin accessibility changes in bone marrow derived macrophages (BMDMs) isolated from Baf60a KO or WT mice |
| GSE224668 |
Myeloid BAF60a Deficiency Alters Metabolic Homeostasis and Exacerbates Atherosclerosis |
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| Relations |
| BioSample |
SAMN36745529 |
| SRA |
SRX21181218 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7666459_18134-282-01_S0_L001_peaks.narrowPeak.gz |
709.8 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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