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Status |
Public on Jul 01, 2024 |
Title |
5xFAD MetX04 negative microglia - ATAC_rep1 |
Sample type |
SRA |
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|
Source name |
FACS-sorted microglia
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 age: 10m cell type: FACS-sorted microglia genotype: 5xFAD treatment: MetoxyX04
|
Treatment protocol |
N.A.
|
Growth protocol |
Microglia were non-enzymatically isolated from a WT, 5xFAD, and IRF8KO brain.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
FACS-sorted microglia were lysed in NP-40 lysis buffer. As manufacturer's protocol, the isolated nuclei were tagmented using the Nextera DNA library prep kit (Illumina). The library was amplified by 9-14-cycle PCR and size-selected.
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|
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 550 |
|
|
Description |
5xFADMG_10m_F_ATAC_merge_SeqDepthNorm.bw
|
Data processing |
Basecalls performed using bcl2fastq without the acceptance of index mismatch After removing the adapter and low-quality sequences, the data were aligned to the mm10 genome with Bowtie2. Peaks were called on aligned sequences using MACS2 v2.2.7.1 with -p 0.01 --nomodel --shift -37 --extsize 73 -B --SPMR --keep-dup all options. All peaks were further filtered with less than 0.01 irreversible differential rates. The bigwig files were generated with Deeptools to visualize the RPGC-normalized, average peaks of each genotype. Assembly: mm10 Supplementary files format and content: Peak files (.narrowpeak) consist of peak regions and tag density generated by MACS2 Supplementary files format and content: A bigwig file contains RPGC-normalized, average peaks of each genotype.
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|
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Submission date |
May 02, 2024 |
Last update date |
Jul 01, 2024 |
Contact name |
Keita Saeki |
E-mail(s) |
keita.saeki@nih.gov
|
Organization name |
NIH/NICHD
|
Street address |
6 Center Drive
|
City |
Bethesda |
State/province |
Maryland |
ZIP/Postal code |
20892 |
Country |
USA |
|
|
Platform ID |
GPL21626 |
Series (2) |
GSE266421 |
Genome-wide open chromatin status in WT and IRF8KO microglia |
GSE266424 |
IRF8 defines the epigenetic landscape in postnatal microglia, thereby directing their transcriptome programs - additional datasets |
|
Relations |
BioSample |
SAMN41164154 |
SRA |
SRX24435117 |