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Sample GSM686641 Query DataSets for GSM686641
Status Public on May 19, 2011
Title KSL cells, biological replicate 2
Sample type RNA
Source name KSL cells
Organism Mus musculus
Characteristics cell type: KSL cells
genetic background: C57BL/6
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using an ISOGEN reagent (Nippon Gene).
Label Biotin
Label protocol Biotinylated cRNA were prepared from the purified total RNA equivalent to 3,000 cells with a Two-Cycle cDNA Synthesis Kit and 3'-Amplification Reagents for IVT Labeling (Affymetrix).
Hybridization protocol Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45˚C on GeneChip Mouse Genome 430 2.0 Array (Affymetrix). Arrays were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using Affymetrix GeneChip Scanner 3000 7G.
Description KSL cells purified by cell sorting
Data processing The data were analyzed with GeneChip Operating Softwere version 1.4 (GCOS1.4, Affymetrix) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
Submission date Mar 07, 2011
Last update date May 19, 2011
Contact name Hitoshi Ichikawa
Phone +81-3-3542-2511
Fax +81-3-3248-1631
Organization name National Cancer Center Research Institute
Lab Genetics Division
Street address 5-1-1 Tsukiji, Chuo-ku
City Tokyo
ZIP/Postal code 104-0045
Country Japan
Platform ID GPL1261
Series (2)
GSE27786 Gene expression profile of mouse hematopoietic cells
GSE27787 Hematopoietic cells and stem cells

Data table header descriptions
VALUE MAS 5.0 signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)

Data table
AFFX-BioB-5_at 71.417 P 0.00227496
AFFX-BioB-M_at 84.8958 P 0.000340305
AFFX-BioB-3_at 57.7705 P 0.000126798
AFFX-BioC-5_at 179.791 P 0.00110197
AFFX-BioC-3_at 233.811 P 4.42873e-05
AFFX-BioDn-5_at 455.599 P 4.42873e-05
AFFX-BioDn-3_at 820.316 P 0.000169227
AFFX-CreX-5_at 2467.08 P 5.16732e-05
AFFX-CreX-3_at 2918.21 P 4.42873e-05
AFFX-DapX-5_at 0.915991 A 0.5
AFFX-DapX-M_at 4.42403 A 0.470241
AFFX-DapX-3_at 6.839 A 0.382599
AFFX-LysX-5_at 0.547002 A 0.834139
AFFX-LysX-M_at 1.00209 A 0.86866
AFFX-LysX-3_at 3.33195 A 0.123572
AFFX-PheX-5_at 0.569416 A 0.960339
AFFX-PheX-M_at 7.76596 A 0.354453
AFFX-PheX-3_at 3.29051 A 0.559354
AFFX-ThrX-5_at 0.978693 A 0.891021
AFFX-ThrX-M_at 0.505066 A 0.876428

Total number of rows: 45101

Table truncated, full table size 1378 Kbytes.

Supplementary file Size Download File type/resource
GSM686641_KSL_2-S.CHP.gz 245.3 Kb (ftp)(http) CHP
GSM686641_KSL_2.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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