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| Status |
Public on Jan 28, 2022 |
| Title |
190218Mk3_Ifng |
| 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: IFNg
replicate: rep1
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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 |
total RNA |
| Extraction protocol |
Cells were collected with qiazol (Qiagen) and stored at -80°C until further processing. RNA was extracted with the miRNeasy mini kit (Qiagen) according to manufacturer’s instructions. Contaminating DNA was degraded by treatment of the samples with RNase-free DNase (Qiagen) in column.
0.1-1ug of RNA was used to make RNA-seq libraries with the TruSeq Stranded Total RNA Library Prep Gold kit (Illumina) according to manufacturer's instructions. Four replicates per condition were performed with primary OPCs obtained from different litters. Libraries were sequenced on an Illumina Novaseq 6000 with a 150-8-8-150 read set-up.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Bulk RNA-seq samples were preprocessed for adapter/quality trimming and then aligned to the transcriptome using STAR with EnsEMBLv75 annotations. Filtered fastq files were used in Salmon 0.8.2 to recover raw reads counts and transcripts per million (TPM) values per transcript and gene. The differential gene expression analysis was performed from the estimated gene counts with Deseq2.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: P13154_100*_quant.sf: Contains the tab-separated table of normalized abundance measurements output from Salmon at transcript level. With EnsEMBL75 mm10 annotation, for each of the 12 samples. Including transcript length, estimated number of counts and TPM.
Supplementary_files_format_and_content: Dexa_DGE_deseq2.Gene.res.txt: Differential gene expression output from Deseq2 using as reference the 3 replicates of the Ctrl samples compared to the 3 replicates of the Dexa samples.
Supplementary_files_format_and_content: Ifng_Dexa_DGE_deseq2.Gene.res.txt: Differential gene expression output from Deseq2 using as reference the 3 replicates of the IFNg samples compared to the 3 replicates of the Dexa samples.
Supplementary_files_format_and_content: Ifng_DGE_deseq2.Gene.res.txt: Differential gene expression output from Deseq2 using as reference the 3 replicates of the Ctrl samples compared to the 3 replicates of the IFNg samples.
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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 |
| GSE173182 |
A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis [RNA-seq IFNg_vs_Dexa_vs_Ctr] |
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| Relations |
| BioSample |
SAMN18840938 |
| SRA |
SRX10664751 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5261605_P13154_1003_quant.sf.gz |
1.8 Mb |
(ftp)(http) |
SF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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