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Sample GSM703149 Query DataSets for GSM703149
Status Public on Apr 08, 2011
Title GCB LRF F/+ mb1-Cre+ #2
Sample type RNA
 
Source name Germinal center B cells of control mouse
Organism Mus musculus
Characteristics cell type: FACS-sorted germinal center B cells (B220+CD19+CD38-Fas+)
genetic background: mixed including C57BL/6 and Zbtb7a-neo/+N1
genotype: LRF Flox/+ mb1-Cre+ (LRF heterozygous)
age: 10 wk
Treatment protocol LRF knockout (LRF Flox/Flox mb-1 Cre+) and control (LRF Flox/+ mb-1 Cre+) mice (4 each) were immunized with sheep red blood cells (SRBCs), and GCB cells were FACS-sorted 7 d later.
Extracted molecule total RNA
Extraction protocol RNA samples were prepared using the Absolutely RNA Microprep kit (Stratagene).
Label biotin
Label protocol Synthesis and labelling of cDNA targets, hybridization and scanning of GeneChips were carried out by the Microarray Core Facility at City of Hope. Due to limited starting material, we used a modified two-cycle amplification protocol. Briefly, cRNA was generated using 10 ng total RNA, according to the manufacturer's protocol, by using Affymetrix's GeneChip Whole Transcript Sense Target Labelling Assay in the first cycle of amplification. The cRNA was subjected to the RiboMinus kit (Invitrogen) to remove rRNA.
 
Hybridization protocol The resulting cRNA was used as the template for another round of amplification using the sense target labelling assay kit. Hybridization cocktails containing 5.5 μg of fragmented, end-labelled cDNA were prepared and applied to GeneChip Mouse Gene 1.0 ST arrays (GPL6246, Affymetrix). Hybridization was performed for 16 h, and the arrays were washed and stained with the GeneChip Fluidics Station 450 using FS450_0007 script
Scan protocol Arrays were scanned at 5 μm resolution using the Affymetrix GCS 3000 7G and GeneChip Operating Software v. 1.4 to generate CEL intensity files.
Description 10 wks old mice. 7 days after immunization.
Gene expression data from FACS-sorted germinal center B cells (B220+CD19+CD38-Fas+)
Data processing The raw data is normalized by Robust Multi-array Average(RMA) using Affymetrix Expression Console
 
Submission date Apr 07, 2011
Last update date Apr 08, 2011
Contact name Takahiro Maeda
Organization name Beckman Research Institute of the City of Hope
Department Hematopoietic Stem Cell and Leukemia Research
Lab Maeda
Street address 1500E Duarte Rd
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
 
Platform ID GPL6246
Series (1)
GSE28449 Expression data from control and LRF-deficient mouse germinal center B cells

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
10344614 9.047639
10344616 3.047555
10344620 5.575285
10344622 8.577913
10344624 9.299137
10344633 10.91356
10344637 8.56476
10344653 5.92461
10344658 7.151617
10344674 4.094584
10344679 6.48281
10344707 8.811434
10344713 10.9153
10344715 6.606749
10344717 4.711918
10344719 7.294041
10344721 2.639839
10344723 8.27159
10344725 8.755417
10344741 11.59743

Total number of rows: 35556

Table truncated, full table size 621 Kbytes.




Supplementary file Size Download File type/resource
GSM703149_C535_MoGene-1.0_ST_2_HZ2_.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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