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Sample GSM3500934 Query DataSets for GSM3500934
Status Public on Dec 05, 2018
Title nonTX,CD25-
Sample type RNA
Source name no thymectomy, CD25-
Organism Mus musculus
Characteristics tissue: spleen
cell type: T cells
cell markers: CD4+, CD25-
treatment: no thymectomy
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from mouse ear and purified using the RNeasy Mini Kit (Qiagen). Samples are pooled from 4 mice for each treatment. The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 150 ng RNA using the One-Color Low Input Quick Amp Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
Hybridization protocol 1650 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 55 µl containing 25x Agilent fragmentation buffer and 10x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 55 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent SurePrint GE Unrestricted Microarrays (G2519F) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 8x60K array slides (Scan Area 61x21.6 mm, Scan resolution 3 µm, Dye channel is set to Green and Green PMT is set to 100%).
Data processing The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Submission date Dec 04, 2018
Last update date Dec 05, 2018
Contact name Naozumi Ishimaru
Phone 0886337328
Organization name Tokushima University Graduate School
Department Oral Molecular Pathology
Street address Kuramoto
City Tokushima
ZIP/Postal code 7708504
Country Japan
Platform ID GPL11202
Series (1)
GSE123332 Follicular helper T cells enhance autoimmunity through Ascl-2 in a murine model for Sjögren’s syndrome

Data table header descriptions
VALUE Normalized signal intensity (Shift to 75 percentile).

Data table
(+)E1A_r60_1 0.08551979
(+)E1A_r60_3 0.01829338
(+)E1A_r60_a104 0.014005661
(+)E1A_r60_a107 0.022975445
(+)E1A_r60_a135 0.023727894
(+)E1A_r60_a20 0.18920565
(+)E1A_r60_a22 0.09338379
(+)E1A_r60_a97 0.088945866
(+)E1A_r60_n11 0.079214096
(+)E1A_r60_n9 0.08707857
(-)3xSLv1 0.002305985
A_51_P100034 -0.29825974
A_51_P100174 -0.040060997
A_51_P100208 0.013037205
A_51_P100289 -0.030837536
A_51_P100298 0.13219595
A_51_P100309 -0.071097374
A_51_P100327 0.1215148
A_51_P100347 -0.45000935
A_51_P100519 0.010121346

Total number of rows: 39485

Table truncated, full table size 965 Kbytes.

Supplementary file Size Download File type/resource
GSM3500934_US10053769_252665513090_S01_GE1_107_Sep09_1_3.txt.gz 2.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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