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Sample GSM5819648 Query DataSets for GSM5819648
Status Public on Jan 14, 2023
Title B_cell_Aff3het_rep2
Sample type RNA
 
Source name Aff3+/- Spleen B cell, LPS/IL4_3d, replicate 2
Organism Mus musculus
Characteristics genotype: Aff3+/-
Treatment protocol CD43-negative B cells were purified from Aff3+/- or Aff3-/- mouse spleen, and cultured in the presence of 10 ug/mL LPS and 10 ng/mL IL-4 for 3 days, and total RNA was extracted from these cells and used for the analysis.
Extracted molecule total RNA
Extraction protocol RNA was prepared using RNeasy plus Mini kit (Qiagen) following the manufacturer's recommendations. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 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 4x44K array slides (Scan Area 61x21.6 mm, Scan resolution 5 µm, Dye channel was set to Green and Green PMT was set to 100%).
Description Gene expression after 3 days culture with LPS/IL4 of Aff3+/- mouse B cells
Data processing The scanned images were analyzed with Feature Extraction Software 10.7.1.1 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028282_D_F_20110531) to obtain background subtracted and spatially detrended processed signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
 
Submission date Jan 14, 2022
Last update date Jan 14, 2023
Contact name Koji Yasutomo
E-mail(s) yasutomo@tokushima-u.ac.jp
Organization name Tokushima University
Department Graduate school of Biomedical Sciences
Lab Immunology and Parasitology
Street address 3-18-15 Kuramoto-cho
City Tokushima
ZIP/Postal code 770-8503
Country Japan
 
Platform ID GPL11202
Series (1)
GSE193735 Effects on gene expression by Aff3-deficiency

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
DarkCorner -0.05157566
A_55_P1991598 -0.0726881
A_55_P1980764 0.0689373
A_51_P128876 0.1592412
A_55_P2121042 -0.040509224
A_52_P219230 -0.07311058
A_51_P207591 -0.038959503
A_55_P2131920 -0.04675579
A_55_P2101944 0.1068573
A_51_P309854 -0.15072632
A_51_P234359 -0.045073032
A_51_P487813 0.15212679
A_52_P613977 0.17490959
A_55_P1957209 -0.07856846
A_52_P549166 -0.08090305
A_55_P2096028 -0.08341503
A_55_P2052210 -0.04647875
A_51_P128987 -0.004321098
A_51_P111223 -0.09005737
A_51_P267969 0.08809948

Total number of rows: 25372

Table truncated, full table size 628 Kbytes.




Supplementary file Size Download File type/resource
GSM5819648_Aff3het_2.txt.gz 2.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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