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Sample GSM2102081 Query DataSets for GSM2102081
Status Public on Jun 22, 2016
Title TKZP4
Sample type RNA
 
Source name fibroblast-derived iPS cells
Organism Homo sapiens
Characteristics cell type: induced pluripotent stem cells
Treatment protocol The cells were collected by picking up clumps manually.
Growth protocol All cells were cultured on irradiated mouse embryonic fibroblasts in standard human pluripotent stem cell media with basic fibroblast growth factor.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from semi-confluent cells using RNeasy mini kit (Quiagen).
Label Cy3
Label protocol cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).
 
Hybridization protocol cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Human Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.
Scan protocol The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).
Data processing The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. In addition, the raw signal intensities of two samples were normalized by the quantile algorithm with the Bioconductor.
 
Submission date Mar 31, 2016
Last update date Apr 23, 2018
Contact name Takafumi Hiramoto
E-mail(s) takafumiester@gmail.com
Organization name University of Washington
Department Division of Hematology
Street address 1959 NE Pacific Street, HSB K-260
City Seattle
ZIP/Postal code 98195-7720
Country USA
 
Platform ID GPL17077
Series (2)
GSE79759 Human embryonic stem cells vs. fibroblast-derived iPS cells
GSE79762 New non-transmissible measles virus vector for establishment of iPS cells
Relations
Reanalyzed by GSE113533

Data table header descriptions
ID_REF
VALUE quantile normalized signal, non-log scaled
ABS_CALL

Data table
ID_REF VALUE ABS_CALL
A_19_P00315452 733.2507 P
A_19_P00315459 101.68208 P
A_19_P00315482 34.03532 P
A_19_P00315492 7.497672 A
A_19_P00315493 7.909562 A
A_19_P00315502 688.80425 P
A_19_P00315506 337.8772 P
A_19_P00315518 3.9966465 A
A_19_P00315519 3.9233365 A
A_19_P00315524 8083.1195 P
A_19_P00315528 111.60876 P
A_19_P00315529 111.93036 P
A_19_P00315538 3.852037 A
A_19_P00315541 42.88208 P
A_19_P00315543 24.120825 P
A_19_P00315550 145.9235 P
A_19_P00315551 68.28385 P
A_19_P00315554 4.168533 A
A_19_P00315581 3385.5845 P
A_19_P00315583 58.17007 P

Total number of rows: 50599

Table truncated, full table size 1239 Kbytes.




Supplementary file Size Download File type/resource
GSM2102081_US11030397_253949424944_S01_GE1_107_Sep09_2_1.txt.gz 12.3 Mb (ftp)(http) TXT
Processed data included within Sample table

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