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Sample GSM188611 Query DataSets for GSM188611
Status Public on May 17, 2007
Title thymocytes_DN2_1
Sample type RNA
 
Source name double negative thymocytes subset DN2
Organism Mus musculus
Characteristics Strain:C57BL/6, Gender:female, Age:5-6 weeks,
Treatment protocol FACS sorting
All antibodies used for cell sorting were purchased from BD Pharmingen (San Diego, CA). Thymocytes were harvested from 5- to 6-week-old female C57BL/6 mice. Four independent cell sortings were performed and four mice were sacrificed for each experiment. Before cell sorting, CD4+ cells and CD8+ cells were depleted using the MACS LD system (Miltenyi Biotec, Bergisch Gladbach, Germany). The remaining fraction was stained with anti-CD44 and anti-CD25 antibodies conjugated to FITC or PerCP-Cy5.5, respectively, and also with PE-conjugated antibodies to CD4, CD8, CD3, NK1.1, and TCRgamma-delta and sorted using a FACSAria cell sorter (BD Bioscience). DN2, DN3, and DN4 subsets were identified as FITC+PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5+, FITC-PE-PerCP-Cy5.5- populations, respectively.
Extracted molecule total RNA
Extraction protocol RNA was extracted from sorted cells using RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instruction.
Label biotin
Label protocol Biotin-labeled cRNA probes were prepared using Two-Cycle cDNA synthesis kit® (Affymetrix®, Santa Clara, CA), according to Affymetrix protocol.
 
Hybridization protocol Following fragmentation, Biotin-labeled cRNA was hybridized to the Mouse Genome 430 2.0 Array® (Affymetrix®) for 16 h at 45°C as recommended by the manufacturer. Washing was performed using an automated fluidics workstation, and the array was immediately scanned with GeneChip Scanner 3000 7G.
Scan protocol The array wasscanned with GeneChip Scanner 3000 7G.
Description Cell source of DN2_1, DN3_1, and DN4_1 are identical.
Cell source of DN2_2, DN3_2, and DN4_2 are identical.
Cell source of DN2_3, DN3_3, and DN4_3 are identical.
Cell source of DN2_4, DN3_4, and DN4_4 are identical.
Each cell sorce was derived from four mice.
Data processing Expression data were extracted from image files produced on Affymetrix® GeneChip Operating Software 1.0® (GCOS®).
 
Submission date May 13, 2007
Last update date Aug 28, 2018
Contact name Masahito Kawazu
E-mail(s) mkawz-tky@umin.ac.jp
Fax +81-3-5804-6261
Organization name University of Tokyo Hospital
Department Department of Hematology and Oncology
Street address Hongo 7-3-1
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-8655
Country Japan
 
Platform ID GPL1261
Series (1)
GSE7784 Expression profiling of double negative thymocytes
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE signal intensity
ABS_CALL call
DETECTION P-VALUE significance of call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 107.944 P 0.000753643
AFFX-BioB-M_at 157.483 P 0.000296708
AFFX-BioB-3_at 119.236 P 7.00668e-05
AFFX-BioC-5_at 336.361 P 6.02111e-05
AFFX-BioC-3_at 461.509 P 5.16732e-05
AFFX-BioDn-5_at 733.409 P 4.42873e-05
AFFX-BioDn-3_at 1339.31 P 5.16732e-05
AFFX-CreX-5_at 3955.5 P 5.16732e-05
AFFX-CreX-3_at 4986.24 P 4.42873e-05
AFFX-DapX-5_at 18.3998 P 0.0032123
AFFX-DapX-M_at 312.126 P 0.000753643
AFFX-DapX-3_at 657.814 P 5.16732e-05
AFFX-LysX-5_at 16.2568 A 0.116113
AFFX-LysX-M_at 53.9402 P 0.0044838
AFFX-LysX-3_at 98.1441 P 0.000126798
AFFX-PheX-5_at 12.3699 A 0.0894781
AFFX-PheX-M_at 49.4698 P 0.000146581
AFFX-PheX-3_at 105.44 P 9.4506e-05
AFFX-ThrX-5_at 15.455 A 0.340661
AFFX-ThrX-M_at 46.9503 P 0.00141043

Total number of rows: 45101

Table truncated, full table size 1381 Kbytes.




Supplementary file Size Download File type/resource
GSM188611.CEL.gz 6.2 Mb (ftp)(http) CEL
GSM188611.CHP.gz 246.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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