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| Status |
Public on Jul 24, 2024 |
| Title |
Old microglia_lesion WM_rep1 |
| Sample type |
SRA |
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| Source name |
LesionWM, Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: LesionWM, Brain
cell type: Cd11b+ microglia
Sex: male
age: 20 months old
strain: C57Bl/6J
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cd11b+ cells were isolated using Magnetic activated cell sorting (MACS) and cryopreserved with 5% DMSO to allow slow cooling rate inorder to minimise cell lysis. Further, viable cells were prepared for library using the original procedure (Buenrostro et al., 2013) with some added modifications for frozen cells (Fujiwara et al., 2019).Briefly, cell pellets were re-suspended in ice-cold lysis buffer (10 mM Tris-Cl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, and 0.1 % (v/v) Igepal CA-630) to extract the cell nuclei
The library of transposed DNA fragments was prepared according to (Buenrostro et al., 2013).DNA was purified with the ZymoResearch DNA Clear & Concentrator TM-5 kit and eluted in 10 µl of elution buffer. qPCR was then performed to determine the additional number of PCR cycles required for the final library. The profiles of libraries were assessed with the Bioanalyzer2100.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
FastQC was used to check the quality of raw fastq files
ATAC-seq reads were trimmed for Nextera transposase adapters and reads <20 bp with quality cutoff 20 was done using Cutadapt.
The trimmed fastq files were aligned to the mm10 genome using bowtie2 using default parameters. The mapped reads were further filtered for mitochondrial reads, reads that are not properly paired and with low mapping quality (phred scale >=30) using BAM tools.
Peak calling was performed using MACS2 (‘- -nonmodel - - shift-100 - -extsize 200’) in Galaxy. Detection of differential binding sites was done using csaw .
Bigwig files were generated from the bedgraph treatment files generated by MACS2 using the command wigtoBigWig in Galaxy. The replicates in each condition were merged using the Bigwig merge to generate a combined bigwig file for each condition.
Assembly: mm10
Supplementary files format and content: bigWig
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| Submission date |
Apr 20, 2023 |
| Last update date |
Jul 24, 2024 |
| Contact name |
Vini Tiwari |
| E-mail(s) |
v.tiwari@tum.de
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| Organization name |
Technical University Munich, (TUM), Deutsches Zentrum für Neurodegenerative Erkrankungen
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| Street address |
Feodor Lynen Straße 17
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| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
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| Platform ID |
GPL18480 |
| Series (1) |
| GSE230187 |
Microglia response upon demyelinating injury [ATAC-seq] |
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| Relations |
| BioSample |
SAMN34268170 |
| SRA |
SRX20026670 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7191403_Old_Rep1.bigwig |
612.1 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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