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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 02, 2024 |
| Title |
Sample 7_H3K9ac7, WT |
| Sample type |
SRA |
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| Source name |
Microglia cells
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| Organism |
Mus musculus |
| Characteristics |
cell type: Microglia cells
genotype: WT
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Anti H3K9ac ChIP-seq were performed using using the iDeal ChIP-seq kit for Histones (Diagenode, Cat.#C01010059) and NEBNext® UltraTM II DNA Library Prep Kit for Illumina® (NEB, Cat.#E7103S). Briefly, microglia were sorted from Itgb8fl/fl;Emx1Cre mouse brain cortex and were pooled from different individuals with same genotype to achieve > 200 k cells per replicates. The microglia were fixed with 1% formaldehyde at 20℃ for 8 min then quenched with 0.125 M Glycine. The nuclei were isolated and sonicated using a Diagenode disruptor for 20 cycles (30 seconds “ON”, 30 seconds “OFF”, high power). The chromatin fragments were enriched using 2 ul of anti-H3K9ac antibody (Millipore, 07-352) per reaction.
The ChIPed DNA was purified and processed for library preparation. The ChIP DNA libraries were size selected using SPRIselect beads (Beckman Coulter, Cat.#B23317) and quantified using Agilent 2100 Bioanalyzer and Qubit (Invitrogen, Cat.#Q33238). The pooled libraries were then sent to Azenta Life Sciences for paired-end sequencing (2x150 bp) on Illumina HiSeq platform.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Samples were processed according to Smart-Seq2 protocol and sequenced on Illumina sequencers.
Reads in FASTQ were aligned to mm10 mouse genome using bowtie2, subsequently filtered using sambamba and indexed using samtools.
Significant peaks were determined using MACS2. Master peakfile was created using bedtools and counts per significant peak were extracted from sorted bam files.
Extracted counts were analysed using DESeq2.
Assembly: mm10
Supplementary files format and content: Bigwig file format, which was created from sorted BAM files and normalization against mouse genome length using deeptools.
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| Submission date |
Sep 01, 2023 |
| Last update date |
Sep 02, 2024 |
| Contact name |
Gabriel McKinsey |
| E-mail(s) |
gabriel.l.mckinsey@gmail.com
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| Organization name |
University of California San Francisco
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| Department |
Pediatrics
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| Lab |
Arnold
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| Street address |
1550 4th St. Room 545E
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| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94107 |
| Country |
USA |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE242220 |
Radial glia promote microglial development through aVb8 -TGFb1 signaling [ChIP-seq] |
| GSE242221 |
Radial glia promote microglial development through aVb8 -TGFb1 signaling |
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| Relations |
| BioSample |
SAMN37239892 |
| SRA |
SRX21600822 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7755838_H3K9ac7.bw |
78.3 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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