NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM183455 Query DataSets for GSM183455
Status Public on Jan 11, 2008
Title T cell_No IL-2_4 hour_rep1
Sample type RNA
 
Source name T cells, IL-2 starved for 14 hours followed by additional IL-2 starvation for 4 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 additional IL-2 starvation for 4 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 additional IL-2 starvation for 4 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 Apr 20, 2007
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 483.1 P 0.000662
AFFX-BioB-M_at 765.4 P 0.000044
AFFX-BioB-3_at 487.4 P 0.000044
AFFX-BioC-5_at 490.2 P 0.000225
AFFX-BioC-3_at 731.8 P 0.000044
AFFX-BioDn-5_at 3910.7 P 0.000044
AFFX-BioDn-3_at 5991.6 P 0.00007
AFFX-CreX-5_at 21120.8 P 0.000052
AFFX-CreX-3_at 27329 P 0.000044
AFFX-DapX-5_at 3574 P 0.000044
AFFX-DapX-M_at 10267.3 P 0.000052
AFFX-DapX-3_at 13794.1 P 0.000044
AFFX-LysX-5_at 837.2 P 0.000044
AFFX-LysX-M_at 1029.2 P 0.000044
AFFX-LysX-3_at 2763.9 P 0.000044
AFFX-PheX-5_at 1125.8 P 0.000044
AFFX-PheX-M_at 1683.1 P 0.000044
AFFX-PheX-3_at 1678.6 P 0.000044
AFFX-ThrX-5_at 1035.7 P 0.00007
AFFX-ThrX-M_at 1975.6 P 0.000044

Total number of rows: 45101

Table truncated, full table size 1206 Kbytes.




Supplementary file Size Download File type/resource
GSM183455.CEL.gz 3.6 Mb (ftp)(http) CEL
GSM183455.EXP.gz 329 b (ftp)(http) EXP
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap