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| Status |
Public on Aug 25, 2018 |
| Title |
SS2_16_290_A12_R1 Control |
| Sample type |
SRA |
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| Source name |
Pdgfra-Cre-LoxP-GFP
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| Organism |
Mus musculus |
| Characteristics |
strain: CD1
tissue: Spinal Cord
celltype: GFPpositive FACS sorted cells from spinal cord
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| Treatment protocol |
For the induction of chronic EAE, animals were injected subcutaneously with an emulsion in MOG35-55 in complete Freud’s adjuvant (CFA) (EK-2110 kit from Hooke Laboratories) followed by the administration of pertussis toxin in PBS (0,2μg per animal), for two consecutive days (all according to manufacture’s instructions). Spinal cords and cerebellum were collected at the chronic stage of the disease with clinical score=3 representing limp tail and complete paralysis of hind legs. Animals that did not reach this clinical score were not analysed in this study. Additional animals were injected subcutaneously with a CFA emulsion (CK-2110 kit from Hooke Laboratories) and used as controls.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were isolated from the spinal cord of P90 Pdgfra-H2B-GFP and Pdgfra-Cre-LoxP-GFP mice. Tissue was then dissociated into a single cell suspension, as previously described in Marques et al 2016, with some modifications. Mice were perfused with oxygenated cutting solution (87 mM, NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 75 mM sucrose, 20 mM glucose, 1 mMCaCl2, and 2 mM MgSO4) and the brain was quickly dissected and dissociated using the Adult brain dissociation kit from Miltenyi (130-107-677) following the manufacturer’s instructions (red blood cells removal step was not included). After debris removal, cell suspension was filtered with 30μm filter (Partec) and processed by FACS sorting. Spinal cord single GFP+ cells were selected in a BD Influx sorter and collected into a 384 plate for SmartSeq2, according to procedures described in.
SmartSeq2 raw data was processed according to procedures described in S. Picelli et al., Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10, 1096-1098 (2013)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Complete Freund’s adjuvant
SS2_16_290_counts-ercc.tab
SS2_16_290_counts.tab
SS2_16_290_rpkms-ercc.tab
SS2_16_290_rpkms.tab
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| Data processing |
SmartSeq2 raw data was processed according to procedures described in S. Picelli et al. 1096-1098 (2013)
Smart-seq2 for sensitive full-length transcriptome profiling in single cells. Nat Methods 10
Genome_build: mm10
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| Submission date |
May 02, 2018 |
| Last update date |
Aug 25, 2018 |
| Contact name |
David van Bruggen |
| E-mail(s) |
david.van.bruggen@ki.se
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| Organization name |
Karolinska Institutet
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| Department |
MBB
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| Lab |
Unit MolNeuro
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| Street address |
Scheeles väg 2
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| City |
Stockholm |
| State/province |
Stockholm |
| ZIP/Postal code |
17177 |
| Country |
Sweden |
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| Platform ID |
GPL21273 |
| Series (1) |
| GSE113973 |
*Possible corruption in count data files-update in progress* Disease-specific oligodendrocyte lineage cells express immunoprotective and adaptive immunity genes in multiple sclerosis |
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| Relations |
| BioSample |
SAMN09012529 |
| SRA |
SRX4031204 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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