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| Status |
Public on Jan 28, 2022 |
| Title |
190426Mk2_Dexa |
| Sample type |
SRA |
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| Source name |
Sox10GFP+ OPCs
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| Organism |
Mus musculus |
| Characteristics |
mouse model: EAE
age: P4-P6
cell type: Sox10GFP+ OPCs
condition: Dexa
replicate: rep3
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| Treatment protocol |
Cells were treated with either dexamethasone (1uM, D4902, Sigma) or IFN-gamma (100ng/ml, 485-MI-100, R&D) for 48 hours.
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| Growth protocol |
Brains from P4-P6 mouse pups were collected and dissociated with the neural tissue dissociation kit (P; 130-092-628, Miltenyi). OPCs were obtained by either FACS with Sox10GFP+ selection or by MACS with CD140a microbeads (Cd140a microbead kit, 130-101-547, Miltenyi). For each experiment, multiple brains were pooled to obtain a sufficient number of cells. Cells were seeded on poly-L-lysine (P4707, Sigma) coated plates and grown with OPC proliferation media consisting of DMEM/F12, GlutaMAX (10565018, ThermoFisher Scientific), N2 supplement (17502001, ThermoFisher Scientific) NeuroBrew 21 (130-097-263, Miltenyi), penicillin-streptomycin (15140122, ThermoFisher Scientific), PDGFaa (10ng/ml, 315-17, PeproTech) and bFGF (20ng/ml, 100-18B, PeproTech).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were harvested by TrypLE incubation at 37°C for 5 minutes, collection in cell culture medium and washing in PBS.
ATAC-seq was performed as previously described (Buenrostro et al., 2013) with minor adaptations. Primary OPCs were incubated with TrypLE () at 37°C for 5 minutes and collected in cell culture media. 60,000 cells per condition were washed with PBS and lysed with lysis buffer (containing 0.1% IGEPAL (CA-630), 10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2) and centrifuged for 20 minutes at 500xg and 4°C. Cells were then resuspended in tagmentation mix (dH2O, 2x TD buffer (Wang et al., 2013) and Tn5 enzyme (Picelli et al., 2014)) for 30 minutes at 37°C. The DNA was purified pre- and post-PCR with the MinElute purification kit (Qiagen) and then PAGE purified to remove adapter dimers. Three replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on an Illumina Novaseq 6000 with a 50-8-8-50 read set-up.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
ATACseq (Buenrostro et al., 2013)
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| Data processing |
Bulk ATAC-seq reads were trimmed and aligned with Bowtie2 with TN5 shifted tagAlign for ATAC pipeline. Aligned reads were filtered and duplicates removes (CutAdapt mark duplicates), more detail Kundaje Lab pipeline. Peaks were called with MACS2, with specific parameters for ATAC-seq peak calling (TN5 shifted tagAlign for ATAC pipeline). Peaks signal files, the wig files, were normalize to total number of reads per sample with DeepTools in order to visualize them.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ATAC-seq peaks signal in wig files normalized to total read count.
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| Submission date |
Apr 23, 2021 |
| Last update date |
Jan 28, 2022 |
| Contact name |
Eneritz Agirre |
| Organization name |
Karolinska Institutet
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| Department |
MBB
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| Lab |
Castelo-Branco, Molecular Neurobiology
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| Street address |
Solnavägen 9
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| City |
Stockholm |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE166179 |
A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis |
| GSE173189 |
A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [ATAC-seq] |
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| Relations |
| BioSample |
SAMN18845879 |
| SRA |
SRX10665155 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5261685_P13153_1008_nodup.rpkm_norm.wig.gz |
233.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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