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Sample GSM686637 Query DataSets for GSM686637
Status Public on May 19, 2011
Title CD34(-)KSL hematopoietic stem cells, biological replicate 2
Sample type RNA
Source name CD34(-)KSL hematopoietic stem cells
Organism Mus musculus
Characteristics cell type: CD34(-)KSL hematopoietic stem 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 CD34(-)KSL hematopoietic stem 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)
GSE27785 Gene expression profile of mouse hematopoietic stem 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 225.851 P 0.000169227
AFFX-BioB-M_at 306.965 P 4.42873e-05
AFFX-BioB-3_at 207.764 P 4.42873e-05
AFFX-BioC-5_at 714.295 P 4.42873e-05
AFFX-BioC-3_at 946.453 P 4.42873e-05
AFFX-BioDn-5_at 1577.21 P 4.42873e-05
AFFX-BioDn-3_at 2703 P 4.42873e-05
AFFX-CreX-5_at 8588.34 P 5.16732e-05
AFFX-CreX-3_at 9916.91 P 4.42873e-05
AFFX-DapX-5_at 8.34463 A 0.327079
AFFX-DapX-M_at 8.65837 A 0.340661
AFFX-DapX-3_at 16.3937 A 0.340661
AFFX-LysX-5_at 1.38537 A 0.760937
AFFX-LysX-M_at 1.59127 A 0.876448
AFFX-LysX-3_at 16.1347 P 0.00933744
AFFX-PheX-5_at 1.1649 A 0.891021
AFFX-PheX-M_at 1.60934 A 0.60308
AFFX-PheX-3_at 14.4528 A 0.425962
AFFX-ThrX-5_at 7.66192 A 0.51489
AFFX-ThrX-M_at 14.1866 A 0.131361

Total number of rows: 45101

Table truncated, full table size 1375 Kbytes.

Supplementary file Size Download File type/resource
GSM686637_CD34_-_KSL_4-S.CHP.gz 246.8 Kb (ftp)(http) CHP
GSM686637_CD34_-_KSL_4.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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