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Sample GSM3267170 Query DataSets for GSM3267170
Status Public on Jul 13, 2018
Title Healthy donor 3 CD40L/IL21
Sample type RNA
 
Source name transitional B cells from normal donors
Organism Homo sapiens
Characteristics cell type: transitional B cells
diagnosis: healthy/normal
Treatment protocol B cells were stimulated with recombinant CD40 ligand alone or together with IL-21 (50 ng/mL)
Growth protocol Human transitional B cells were cultured in RPMI1640 containing 10% FCS for 4 days
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol 1 ng of total RNA was used as input for the amplification and labelling of samples using the Affymetrix WT Pico Kit
 
Hybridization protocol 3 µg fragmented, biotin labelled ss-cDNA was hybridised to Affymetrix Human Gene Array version 2.1ST. Samples were hybridised to arrays for 16 hours at 45°C in the Affymetrix GeneTitan Instrument
Scan protocol Arrays were washed and scanned on the Affymetrix GeneTitanand Affymetrix GC3000 scanner instrument as per manufacturers protocol
Description RNA from normal transitional B cells stimulated with CD40L + IL-21
Data processing Bioconductor packages implemented in the R statistical computing environment, version 3.4.1. The file normalized_data_with_all_control_probesets.txt contains the log2 RMA data for all probe sets including control probe sets. The sample data tables include a subset of the control probe sets found on platform GPL23159.
 
Submission date Jul 12, 2018
Last update date Jul 13, 2018
Contact name Stuart Tangye
E-mail(s) s.tangye@garvan.org.au
Phone +61 2 9295 8455
Organization name Garvan Institute of Medical Research
Department Immunology
Street address 384 Victoria St
City Darlinghurst
State/province NSW
ZIP/Postal code 2010
Country Australia
 
Platform ID GPL23159
Series (1)
GSE116999 Identification of differentially expressed genes between control and PIK3CD GOF human activated transitional B cells

Data table header descriptions
ID_REF
VALUE log2 RMA signal

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 1.985539802
AFFX-BkGr-GC04_st 1.793192576
AFFX-BkGr-GC05_st 1.789780489
AFFX-BkGr-GC06_st 1.810714052
AFFX-BkGr-GC07_st 1.885842908
AFFX-BkGr-GC08_st 1.856390617
AFFX-BkGr-GC09_st 1.931828968
AFFX-BkGr-GC10_st 1.961413604
AFFX-BkGr-GC11_st 2.054275734
AFFX-BkGr-GC12_st 2.255956023
AFFX-BkGr-GC13_st 2.341784785
AFFX-BkGr-GC14_st 2.718363124
AFFX-BkGr-GC15_st 2.816845235
AFFX-BkGr-GC16_st 3.670929645
AFFX-BkGr-GC17_st 3.980853617
AFFX-BkGr-GC18_st 4.535856505
AFFX-BkGr-GC19_st 5.043807767
AFFX-BkGr-GC20_st 5.322861564
AFFX-BkGr-GC21_st 5.556683239
AFFX-BkGr-GC22_st 5.88520191

Total number of rows: 24351

Table truncated, full table size 730 Kbytes.




Supplementary file Size Download File type/resource
GSM3267170_Ctl3_T40L_21_Clariom_S_Human_.CEL.gz 1014.6 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data are available on Series record

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