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Sample GSM2628029 Query DataSets for GSM2628029
Status Public on May 15, 2020
Title Arthritic mouse 2
Sample type RNA
 
Source name Spleen
Organism Mus musculus
Characteristics strain: BALB/c
tissue: spleen
cell type: B cell
gender: female
Treatment protocol BALB/c mice were immunized with human PG three times, and after the third treatment B cells were affinity purified from spleens collected from the sacrificed mice.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using Direct-Zol™ RNA MiniPrep Plus kit (Zymo Research, Irvine, CA, USA) treated with Turbo™ DNase (ThermoFisher Scientific, Waltham, MA, USA) and purified with RNA Clean and Concentrator™-5 kit (Zymo).
Label Cy3
Label protocol Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS 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 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) 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 by brief centrifugation.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
Description Gene expression after 10 days of 3rd PG-injection
Data processing The scanned images were analyzed with Feature Extraction Software 9.1 (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 May 15, 2017
Last update date May 15, 2020
Contact name Tibor T Glant
E-mail(s) Tibor_Glant@rush.edu
Organization name Rush University Medical Center
Department Orthopedic Surgery
Lab Molecular Medicine
Street address 1735 West Harrison
City Chicago
State/province IL
ZIP/Postal code 60612
Country USA
 
Platform ID GPL15691
Series (1)
GSE98932 Autoimmune arthritis-associated gene expression in B cells isolated from mice with proteoglycan (PG)-induced arthritis (PGIA)

Data table header descriptions
ID_REF
VALUE Normalized signal intensity

Data table
ID_REF VALUE
ASMM9PARTA025202 6.2129416
ASMM9PARTA030594 7.2947664
ASMM9PARTA020731 8.733963
ASMM9PARTA022696 9.63824
ASMM9PARTA039489 11.932313
ASMM9PARTA036489 5.0182505
ASMM9PARTA025458 4.912828
ASMM9PARTA034156 7.7026052
ASMM9PARTA041233 12.93425
ASMM9PARTA034335 9.865103
ASMM9PARTA023840 6.5931005
ASMM9PARTA039214 4.963893
ASMM9PARTA023516 9.633658
ASMM9PARTA020859 6.685478
ASMM9PARTA032100 8.358686
ASMM9PARTA026111 12.555158
ASMM9PARTA019973 6.3765035
ASMM9PARTA020476 11.025373
ASMM9PARTA026449 6.996956
ASMM9PARTA031767 11.690125

Total number of rows: 13655

Table truncated, full table size 353 Kbytes.




Supplementary file Size Download File type/resource
GSM2628029_Art_B2.txt.gz 2.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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