|
| Status |
Public on Sep 01, 2016 |
| Title |
CD4T_LG_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Lacrimal gland 16w NOD male
|
| Organism |
Mus musculus |
| Characteristics |
tissue: lacrimal gland
subset: CD4T
|
| Treatment protocol |
Lacrimal gland cell suspensions were prepared by mechanical dissociation and enzymatic digestion before FACS cell sorting of epithelial and immune cell subsets. Each cell subset was sorted directly into lysis buffer on a FACSAria cytometer (BD Biosciences). Lysates were stored at -80°C until processing.
|
| Growth protocol |
cells were isolated ex vivo
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNAqueous isolation kit (Ambion). RNA was QC'd using Bioanayzer and all samples had RIN scores >8 except: SAMPLE 145 (RIN=7.8), SAMPLE 108 (RIN=7.7), SAMPLE 111 (RIN=7.2).
|
| Label |
biotin
|
| Label protocol |
The amount of isolated RNA was normalized and automated sample amplification and biotin labeling were carried out using the NuGEN Ovation RNA Amplification system V2, Ovation WB reagent and Encore Biotin module according to manufacturer’s recommendations using an Arrayplex automated liquid handler (Beckman Coulter).
|
| |
|
| Hybridization protocol |
Two micrograms of biotin labeled sscDNA probe were hybridized to Affymetrix GeneChip HT HG-U133+ PM plate arrays with modified conditions as described in (Allaire et al., 2013, PMID: 23289891). Washing and staining of the hybridized arrays were completed as described in the GeneChip Expression analysis technical manual for HT plate arrays using the Genechip Array Station (Affymetrix) with modifications as described in (Allaire et al., 2013, PMID: 23289891).
|
| Scan protocol |
The processed GeneChip plate arrays were scanned using GeneTitan scanner (Affymetrix).
|
| Description |
Gene expression data from ex vivo FACS-sorted T-cell subsets isolated from lacrimal gland and spleen cell suspensions
|
| Data processing |
The data were analyzed with Partek Genomics Suite (Partek) using Affymetrix default analysis settings: RMA background correction, quantile normalization and median polish probeset summarization (log2).
|
| |
|
| Submission date |
Jun 08, 2016 |
| Last update date |
Sep 01, 2016 |
| Contact name |
MICHAEL MINGUENEAU |
| E-mail(s) |
[email protected]
|
| Phone |
8579199313
|
| Organization name |
Biogen
|
| Department |
Immunology
|
| Street address |
115 Broadway
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL11180 |
| Series (1) |
| GSE83113 |
Gene expression analysis of total B, CD4+ T and epithelial cells in lacrimal glands from the NOD mouse model of Sjogren's syndrome |
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