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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Sep 02, 2024 |
| Title |
Sample 14_ATA14, ITGB8KO |
| Sample type |
SRA |
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| Source name |
ATA14
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| Organism |
Mus musculus |
| Characteristics |
cell line: ATA14
cell type: Microglia cells
genotype: ITGB8KO
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq were carried out following the Omni-ATAC-seq protocol (Corces et al., 2017). Briefly, 50 k cortical microglia (CD11b+Fcrls+ Ly-6C–) from Itgb8fl/fl;Emx1Cre mouse brains cells were sorted into Eppendorf tubes by a BD FACSAriaTM II (BD Bioscience). After being washed with cold dPBS, microglia were permeabilized with ATAC-Resuspension Buffer containing 0.1% NP40, 0.1% Tween-20, and 0.01% Digitonin and washed with ATAC-RSB buffer with 0.1% Tween-20.
The isolated microglial nuclei were then incubated in transposition mixture at 37℃ for 60 min. The DNA were purified using a Zymo DNA clean and concentrator-5 kit (Zymo research, Cat.#D4014) and amplified using NEBNext® High-Fidelity 2x PCR Master Mix (NEB, Cat. #M0541s) for 9 cycles. The ATAC 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 |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| 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) |
| GSE242219 |
Radial glia promote microglial development through aVb8 -TGFb1 signaling [ATAC-seq] |
| GSE242221 |
Radial glia promote microglial development through aVb8 -TGFb1 signaling |
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| Relations |
| BioSample |
SAMN37237054 |
| SRA |
SRX21600843 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7755831_ATA14.bw |
73.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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