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Sample GSM140926 Query DataSets for GSM140926
Status Public on Jan 11, 2008
Title T cell_IL-2_1 hour_rep1
Sample type RNA
 
Source name T cells, IL-2 starved for 14 hours followed by IL-2 stimulation for 1 hour
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 1 hour 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 1 hour
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 413.6 P 0.002275
AFFX-BioB-M_at 543.6 P 0.000147
AFFX-BioB-3_at 293.3 P 0.000044
AFFX-BioC-5_at 1134.1 P 0.000169
AFFX-BioC-3_at 1542.4 P 0.000044
AFFX-BioDn-5_at 2414.8 P 0.000044
AFFX-BioDn-3_at 4596.3 P 0.000258
AFFX-CreX-5_at 15548.6 P 0.000052
AFFX-CreX-3_at 18152.3 P 0.000044
AFFX-DapX-5_at 2016.8 P 0.000044
AFFX-DapX-M_at 3911.9 P 0.000195
AFFX-DapX-3_at 3556.7 P 0.000052
AFFX-LysX-5_at 244.6 P 0.000195
AFFX-LysX-M_at 398.3 P 0.011384
AFFX-LysX-3_at 614.7 P 0.000095
AFFX-PheX-5_at 332.3 P 0.000857
AFFX-PheX-M_at 361.1 P 0.000146
AFFX-PheX-3_at 486.6 P 0.000389
AFFX-ThrX-5_at 593 P 0.000258
AFFX-ThrX-M_at 640.9 P 0.000044

Total number of rows: 45101

Table truncated, full table size 1215 Kbytes.




Supplementary file Size Download File type/resource
GSM140926.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM140926.EXP.gz 332 b (ftp)(http) EXP
Processed data included within Sample table

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