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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 21, 2018 |
| Title |
1130S4: EarlyDisease7 |
| Sample type |
SRA |
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| Source name |
Spinal cord
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| Organism |
Mus musculus |
| Characteristics |
strain: mixed C57BL/6J X C3HeJ F1
genotype: (+/+)
gender: F
dox treatment: 2 WKS OFF
phenotype: Early disease
tissue: Spinal cord
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| Growth protocol |
mice were maintained DOX-ON until 8-12 weeks of age. Then diets were maintained as described in the sample table.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were euthanized with ketamine/xylazine cocktail and perfused with ice-cold PBS. Spinal cords were flushed from the spinal column using PBS and placed in ice-cold HBSS with HEPES. Tissue was homogenized using Wheaton tissue grinders to achieve a single cell suspension. The homogenate was centrifuged through a 30% Percoll gradient to remove myelin and enrich for microglia. After washing with FACS buffer (HBSS, HEPES, BSA, EDTA) cells were Fc-blocked (CD16/32, Cat. #101321, Biolegend, San Diego, CA, USA) and stained with CD11b-PE (Cat. #553311, BD Biosciences, MA, USA) and CD45-BV421 (Cat. #103134, Biolegend). DRAQ7 was used for dead cell exclusion. Cells were sorted on an ARIA Fusion Flow Cytometer and collected directly into RNA lysis buffer. RNA was isolated with the RNeasy Micro Kit Plus from Qiagen.
Libraries were constructed using the SMART-Seq Ultra Low-input (Clontech, Mountain View, CA, USA) and NexteraXT kits (Illumina, San Diego, CA, USA). Libraries were sequenced at an average depth of 20 million paired end reads.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Sequence alignments were performed In OmicSoft using OSA4 aligner
Gene expression quantification was performed in OmicSoft using RSEM
Differential gene expression analysis was performed in OmicSoft using DESeq2
Genome_build: mm10 Gencode M6
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| Submission date |
Jan 13, 2018 |
| Last update date |
Feb 22, 2018 |
| Contact name |
Chris Roberts |
| E-mail(s) |
chris.roberts@biogen.com
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| Phone |
6176803235
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| Organization name |
Biogen
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| Street address |
301 Binney St.
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| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (1) |
| GSE109171 |
RNA sequencing of sorted microglia from NEFH-tTa/tetO-hTDP43 transgenic mouse whole spinal cord |
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| Relations |
| BioSample |
SAMN08362258 |
| SRA |
SRX3584284 |
| 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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