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Sample GSM140946 Query DataSets for GSM140946
Status Public on Jan 11, 2008
Title T cell_IL-2_16 hour_rep3
Sample type RNA
 
Source name T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 16 hours
Organism Mus musculus
Characteristics Cytotoxic T lymphocyte cell line CTLL-2, derived from a C57BL/6 mouse, dependent upon IL-2 for growth
Biomaterial provider The American Type Culture Collection (ATCC)
Treatment protocol Cells were cultured in D10 medium in an incubator with 5% CO2 at 37oC to mid-log phase (~2 X 105 cells/mL), and collected by centrifugation, washed with phosphate buffered saline (PBS) (Invitrogen), resuspended at 1 X 106 cells/mL in the medium without IL-2 (IL-2 starvation) and cultured for 14 hours at 37oC with 5% CO2, followed by human rIL-2 (100 U/mL, Chiron) stimulation for 16 hours at 37oC with 5% CO2.
Growth protocol Mouse CTLL-2 cells was maintained in an incubator with 5% CO2 at 37oC in D10 medium (D10 = ATCC modified RPMI-1640 medium (10 mM HEPES, 2 mM L-glutamine, 1 mM Sodium pyruvate, 4.5 g/L glucose, 1.5 g/L sodium bicarbonate), supplemented with 10% fetal bovine serum, 2 mM L-glutamine, 50 U/mL penicillin, 50 mg/mL streptomycin, 1 mM sodium pyruvate, 45 µM ?-mercaptoethanol), and 50 U/mL human rIL-2 (Chiron).
Extracted molecule total RNA
Extraction protocol Cells was collected and washed with PBS, resuspended in PBS before adding RNAlater RNA stabilization solution (Qiagen). Total RNA was isolated using RNeasy Mini Kit (Qiagen) according to manufacturer’s protocol.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ?g total RNA (GeneChip Expression Analysis, Technical Manual (701021 Rev. 5), 2005, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ?g of cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using Affymetrix Gene-Chip scanner 3000.
Description Gene expression data from T cells cultured without IL-2 for 14 hours followed by IL-2 stimulation for 16 hours
Data processing The data were analyzed with Affymetric GeneChip Operating Software (GCOS, version 1.3) using Affymetrix default analysis settings and global scaling as normalization method.
 
Submission date Oct 19, 2006
Last update date Aug 28, 2018
Contact name Zhaoduo Zhang
E-mail(s) zzhang@sandia.gov
Phone 925-294-2513
Fax 925-294-3282
Organization name Sandia National Labs
Department Biosystems
Street address 7011 East Ave
City Livermore
State/province CA
ZIP/Postal code 94551
Country USA
 
Platform ID GPL1261
Series (1)
GSE6085 Expression data from Murine T cell in response to IL-2 at 10 time points in 24 hours after IL-2 treatment
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE GCOS-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 504.7 P 0.000662
AFFX-BioB-M_at 742.7 P 0.000044
AFFX-BioB-3_at 522.5 P 0.00007
AFFX-BioC-5_at 1692.3 P 0.000044
AFFX-BioC-3_at 1605 P 0.000052
AFFX-BioDn-5_at 2847.7 P 0.000044
AFFX-BioDn-3_at 3348.8 P 0.000044
AFFX-CreX-5_at 16262.5 P 0.000052
AFFX-CreX-3_at 20145.1 P 0.000044
AFFX-DapX-5_at 2861.7 P 0.000044
AFFX-DapX-M_at 4142.3 P 0.000052
AFFX-DapX-3_at 5556.6 P 0.000044
AFFX-LysX-5_at 277.1 P 0.00007
AFFX-LysX-M_at 287.6 P 0.000052
AFFX-LysX-3_at 807.9 P 0.00006
AFFX-PheX-5_at 359.4 P 0.00006
AFFX-PheX-M_at 637.4 P 0.000052
AFFX-PheX-3_at 619.1 P 0.000052
AFFX-ThrX-5_at 700.2 P 0.000044
AFFX-ThrX-M_at 922.5 P 0.000044

Total number of rows: 45101

Table truncated, full table size 1206 Kbytes.




Supplementary file Size Download File type/resource
GSM140946.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM140946.EXP.gz 331 b (ftp)(http) EXP
Processed data included within Sample table

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