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| Status |
Public on Sep 29, 2023 |
| Title |
ChIP-Seq Input |
| Sample type |
SRA |
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| Source name |
Primary
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| Organism |
Mus musculus |
| Characteristics |
cell line: Primary
cell type: BMDM
chip antibody: none
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Chromatin immunoprecipitation was performed with the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling, #9003), according to the manufacturer's recommendation. BRG1 (Abcam, ab110641, 1:100 dilution).
The DNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the DNA library was prepared with NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 150bp pair-end reads.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Input
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| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie2.
Peaks were called using MACS3 with parameters: -f BAMPE -g mm --SPMR -q 0.05.
Assembly: mm10
Supplementary files format and content: narrowPeak (except for Input sample)
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| Submission date |
Feb 06, 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
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| 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) |
| GSE224666 |
Genome-wide maps of chromatin state 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 |
SAMN33143131 |
| SRA |
SRX19294699 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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