|
| Status |
Public on Nov 01, 2016 |
| Title |
Control_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Control NP-specific plasma cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
tissue: group: control
|
| Treatment protocol |
The control group is constituted of NP-specific plasma cells sorted from mice primed with NP-dextran and boosted with PBS 60 days later. The boosted group is constituted of NP-specific plasma cells sorted from mice primed with NP-dextran/CpG and boosted with NP-dextran 60 days later
|
| Growth protocol |
Cells have been stimulated in vivo and no further in vitro treatment has been applied before extract preparation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After pelleting, the RNAprotect buffer was replaced by RLT Plus buffer (Qiagen) and the samples were homogenized by vortexing for 1 min. Genomic DNA contamination was removed using gDNA Eliminator spin columns (Qiagen). After addition of ethanol, the samples were applied to RNeasy MinElute spin columns (Qiagen) followed by several washing steps. Finally total RNA was eluted in 12 μl of nuclease-free water. Purity and integrity of the RNA was assessed on the Agilent 2100 Bioanalyzer with the RNA 6000 Pico LabChip reagent set (Agilent).
|
| Label |
biotin
|
| Label protocol |
total RNA was reverse transcribed into double-stranded cDNA in a two-step process, introducing a SPIA tag sequence. Bead-purified cDNA was amplified by a SPIA amplification reaction followed by an additional bead purification. 3 µg of SPIA cDNA were fragmented and terminally biotin-labeled according to the standard Affymetrix protocol
|
| |
|
| Hybridization protocol |
hybridization, washing and staining were performed using an Affymetrix GeneTitan system
|
| Scan protocol |
scanning was performed using an Affymetrix GeneTitan system
|
| Data processing |
Affymetrix CEL files were analyzed in R using the Bioconductor suite of packages. Raw probe signals were background-corrected using the maximum likelihood estimation of the normal-exponential mixture model and normalized using the variance stabilization normalization, followed by quantile normalization. For summarization, probe signals for each probe set of each sample were summarized into a single value using the summarization step of the Robust Multichip Average (RMA) approach
|
| |
|
| Submission date |
Apr 12, 2016 |
| Last update date |
Nov 01, 2016 |
| Contact name |
Simon de Bernard |
| Organization name |
AltraBio
|
| Street address |
30 rue Pré Gaudry
|
| City |
Lyon |
| ZIP/Postal code |
69007 |
| Country |
France |
| |
|
| Platform ID |
GPL21720 |
| Series (1) |
| GSE80216 |
Mature IgM+ plasma cells sense antigen and develop competence for cytokine production upon antigenic challenge |
|
