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Sample GSM1639869 Query DataSets for GSM1639869
Status Public on Mar 21, 2015
Title GMP cells from FLT3/ITD mouse bone marrow
Sample type RNA
Source name FLT3/ITD GMP
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: FLT3/ITD
tissue: bone marrow
cell type: GMP cells
Treatment protocol Mouse bone marrow cells were harvested by flushing the tibia and femur bones with PBS, stained with antibodies and sorted for KSL and GMP cells.
Growth protocol C57BL/6 wild-type and transgenic FLT3/ITD and SmoM2; FLT3/ITD mice were bred in the animal facility. Poly(I:C) was administered via intraperitoneal injections upon weaning.
Extracted molecule total RNA
Extraction protocol RNA from sorted mouse bone marrow cells (KSL and GMP populations) was extracted using the Qiagen Rneasy Micro kit and processed using the RNA amplification protocol described by Affymetrix (Affymetrix 3’ IVT Express Manual).
Label Biotin
Label protocol 100 nanograms of total RNA were used to synthesize first strand cDNA using oligonucleotide probes with 24 oligo-dT plus T7 promoter as primer and the SuperScript Choice System (Invitrogen, Carlsbad, California). Following the double stranded cDNA synthesis, biotinilated anti-sense cRNA was generated through in vitro transcription using the T7 RNA polymerase.
Hybridization protocol 15 ug of the biotinilated cRNA were fragmented at 94 C for 35 min (100mM Tris-acetate, pH 8.2, 500mM KOAc, 150mM MgOAC), and 10ug of total fragmented cRNA were hybridized to the Affymetrix GeneChip arrays for 16hr at 45 C with constant rotation (60 rpm). Affymetrix Fluidics Station 450 was then used to wash and stain the Chips, removing the non-hybridized target and incubating with a streptavidin-phycoerythrin conjugate to stain the biotinilated cRNA. The staining was then amplified using goat IgG as blocking reagent and biotinilated anti-streptavidin antibody (goat), followed by a second staining step with a streptavidin-phycoerythrin conjugate.
Scan protocol Fluorescence was detected using the Affymetrix 3000 GeneArray Scanner with G7 upgrade and image analysis of each GeneChip was done through the Affymetrix GeneChip Command Console 3.4.1 (AGCC) software from Affymetrix, using the standard default settings.
Description Gene expression data from GMP cells of FLT3/ITD mouse bone marrow
Data processing Affymetrix Expression Console (v was used to analyze the data to generate normalized expression values.
affymetrix-algorithm-name = ExpressionStat
affymetrix-algorithm-version = 5.0
program-name = Expression Console
program-id =
Submission date Mar 20, 2015
Last update date Mar 23, 2015
Contact name Yiting Lim
Organization name Johns Hopkins University School of Medicine
Street address 1650 Orleans Street
City Baltimore
State/province MD
ZIP/Postal code 21287
Country USA
Platform ID GPL1261
Series (1)
GSE67134 Expression data from KSL and GMP cells of FLT3/ITD and FLT3/ITD-SmoM2 mice

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

Data table
AFFX-BioB-5_at 2517.97 P 4.42873e-05
AFFX-BioB-M_at 4180.43 P 4.42873e-05
AFFX-BioB-3_at 3738.86 P 4.42873e-05
AFFX-BioC-5_at 6985.07 P 5.16732e-05
AFFX-BioC-3_at 7175.09 P 4.42873e-05
AFFX-BioDn-5_at 15324.6 P 4.42873e-05
AFFX-BioDn-3_at 18831.9 P 4.42873e-05
AFFX-CreX-5_at 36215.2 P 5.16732e-05
AFFX-CreX-3_at 33045.4 P 4.42873e-05
AFFX-DapX-5_at 20.5544 A 0.175328
AFFX-DapX-M_at 4.07765 A 0.904333
AFFX-DapX-3_at 13.0378 A 0.440646
AFFX-LysX-5_at 12.4717 A 0.39692
AFFX-LysX-M_at 7.82291 A 0.340661
AFFX-LysX-3_at 19.6679 A 0.559354
AFFX-PheX-5_at 5.15487 A 0.749204
AFFX-PheX-M_at 4.91093 A 0.724854
AFFX-PheX-3_at 2.93297 A 0.724854
AFFX-ThrX-5_at 9.32649 A 0.529762
AFFX-ThrX-M_at 19.7245 A 0.396902

Total number of rows: 45101

Table truncated, full table size 1391 Kbytes.

Supplementary file Size Download File type/resource
GSM1639869_YLim-RHS-3_FLT3ITDGMP-1a-Mouse430_2_Mouse430_2_.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM1639869_YLim-RHS-3_FLT3ITDGMP-1a-Mouse430_2_Mouse430_2_.mas5.CHP.gz 393.2 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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