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Sample GSM5320053 Query DataSets for GSM5320053
Status Public on May 18, 2021
Title Ba/F3, SPAG9-JAK2(-), rep3
Sample type RNA
 
Source name non-induced Ba/F3 cells not expressing SPAG9-JAK2 (mock Ba/F3)
Organism Mus musculus
Characteristics cell line: Ba/F3
cell type: interleukin-3-dependent murine pro-B cell line
Treatment protocol Ba/F3 cells expressing SPAG9-JAK2 under doxycycline dependent manner were established, and SPAG9-JAK2 protein expression was induced using 500 ng/ml doxycycline.
Growth protocol Ba/F3 cells transduced with SPAG9-JAK2 fusion protein by the Retro-X Tet-on Advanced Inducible System (Takara Bio) were washed twice with phosphate-buffered saline and seeded in triplicate with or without 500 ng/ml doxycycline.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted 48 hours later from Ba/F3 cells with or without expression of SPAG9-JAK2 using an RNeasy Mini Kit (Qiagen, Hilden, Germany), and the quality was checked on a NanoDrop 2000 (Thermo Fisher Scientific) and a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
Label biotin
Label protocol cRNA target synthesis was carried out using a GeneChip 3’IVT PLUS Reagent Kit (Thermo Fisher Scientific).
 
Hybridization protocol Biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 Array (Thermo Fisher Scientific) following the standard protocols.
Scan protocol Hybridized arrays were stained and scanned with a Genechip 3000 7G Scanner (Thermo Fisher Scientific) at the default settings.
Description Gene expression data from non-induced Ba/F3 cells not expressing SPAG9-JAK2 (mock Ba/F3)
Data processing Data were analyzed using Affymetrix Expression Console Software 1.4.1.
 
Submission date May 17, 2021
Last update date May 18, 2021
Contact name Azusa Mayumi
Organization name Kyoto Prefectural University of Medicine
Department Pediatrics
Street address 465, Kajii-cho, Kawaramachi-Hirokoji, Kamigyo-ku
City Kyoto
ZIP/Postal code 602-8566
Country Japan
 
Platform ID GPL1261
Series (1)
GSE174578 SPAG9-JAK2 gene expression array in Ba/F3 cells

Data table header descriptions
ID_REF
VALUE Signal
ABS_CALL indicating whether the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 945.744 P 6.02111e-05
AFFX-BioB-M_at 1203.7 P 4.42873e-05
AFFX-BioB-3_at 755.453 P 4.42873e-05
AFFX-BioC-5_at 2881.28 P 5.16732e-05
AFFX-BioC-3_at 3591.85 P 4.42873e-05
AFFX-BioDn-5_at 5940.62 P 4.42873e-05
AFFX-BioDn-3_at 10202.7 P 7.00668e-05
AFFX-CreX-5_at 25452.6 P 5.16732e-05
AFFX-CreX-3_at 27065.2 P 4.42873e-05
AFFX-DapX-5_at 1060.5 P 4.42873e-05
AFFX-DapX-M_at 2212.98 P 0.00010954
AFFX-DapX-3_at 2526.38 P 4.42873e-05
AFFX-LysX-5_at 149.483 P 9.4506e-05
AFFX-LysX-M_at 216.188 P 0.0044838
AFFX-LysX-3_at 381.083 P 4.42873e-05
AFFX-PheX-5_at 152.579 P 0.000126798
AFFX-PheX-M_at 241.225 P 4.42873e-05
AFFX-PheX-3_at 260.269 P 9.4506e-05
AFFX-ThrX-5_at 213.925 P 0.000509415
AFFX-ThrX-M_at 360.066 P 8.14279e-05

Total number of rows: 45101

Table truncated, full table size 1375 Kbytes.




Supplementary file Size Download File type/resource
GSM5320053_Mock_BaF3_EA1935_04.CEL.gz 3.4 Mb (ftp)(http) CEL
GSM5320053_Mock_BaF3_EA1935_04_scale.CHP.gz 399.0 Kb (ftp)(http) CHP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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