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| Status |
Public on Sep 15, 2021 |
| Title |
Spinalcord_Clostridia_mouse6 |
| Sample type |
RNA |
| |
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| Source name |
Spinal cord, Clostridia, 28 days post-immunization
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6JOlaHsd
tissue: Spinal cord
treatment: Clostridia strains
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spinal cord: Total RNA was isolated using QIAzol lysis reagent (79306, Qiagen) and RNeasy Mini Kit (74104, Qiagen) with on-column DNase digestion (79254, Qiagen) in order to remove any genomic DNA trace according to the manufacturer's instructions. Spleen: RNeasy Mini Kit together with on-column DNase digestion was also used to isolate splenocyte total RNA according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated ds-cDNA were prepared according to the standard Affymetrix (ThermoFisher) protocol from 50 ng total RNA (GeneChip 3' IVT Pico Kit Manual Workflow, user guide).
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| |
|
| Hybridization protocol |
Following fragmentation, 5.5ug of ds-cDNA were hybridized for 16 h at 45ºC on GeneChip Clariom S mouse array plate. Array plate was washed and stained in the Affymetrix Genetitan Instrument (GeneTitan Multichannel system)
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| Scan protocol |
Array plate was scanned using the Genetitan instrument (GeneTitan Multichannel system)
|
| Description |
Gene expression data from EAE mice treated with 17 Clostridia strains
|
| Data processing |
The data were processed and analyzed separately for each tissue. Raw expression values were obtained directly from .CEL files and were processed using the RMA method to get normalized expression values (log2 scale) summarized at the gene level. Different quality checks were performed before and after normalization to ensure that all samples were suitable for differential expression analysis. The analysis to select differentially expressed genes was based on adjusting a linear model with empirical Bayes moderation of the variance. Because batch effects were detected, a batch factor was included in the linear model used for differential expression analysis. Statistical language R (version 3.6.1) and Bioconductor associated packages were used to process and analyze the data.
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| |
|
| Submission date |
Jul 30, 2020 |
| Last update date |
Sep 15, 2021 |
| Contact name |
Carmen Espejo |
| Organization name |
Vall d'Hebron Institute of Research - Centre d'Esclerosi Múltiple de Catalunya
|
| Street address |
Passeig de la Vall d'Hebron, 119-129, Edifici Collserola, Laboratory 149-151
|
| City |
Barcelona |
| ZIP/Postal code |
08035 |
| Country |
Spain |
| |
|
| Platform ID |
GPL24242 |
| Series (1) |
| GSE155438 |
Effect of Clostridia strains on EAE clinical outcome as a therapeutic treatment |
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