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Sample GSM1639868 Query DataSets for GSM1639868
Status Public on Mar 21, 2015
Title KSL cells from wild type bone marrow
Sample type RNA
 
Source name WT KSL
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype/variation: wild type
tissue: bone marrow
cell type: KSL 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 KSL cells of wild type mouse bone marrow
Data processing Affymetrix Expression Console (v 1.2.0.20) 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 = 1.2.0.20
 
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
ID_REF
VALUE ExpressionStat 5.0
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 2659 P 4.42873e-05
AFFX-BioB-M_at 4422.25 P 4.42873e-05
AFFX-BioB-3_at 3722.98 P 4.42873e-05
AFFX-BioC-5_at 7371.41 P 5.16732e-05
AFFX-BioC-3_at 7103.57 P 4.42873e-05
AFFX-BioDn-5_at 15650.1 P 4.42873e-05
AFFX-BioDn-3_at 19609.4 P 4.42873e-05
AFFX-CreX-5_at 35884.3 P 5.16732e-05
AFFX-CreX-3_at 32236.4 P 4.42873e-05
AFFX-DapX-5_at 12.3243 A 0.425962
AFFX-DapX-M_at 2.87662 A 0.834139
AFFX-DapX-3_at 16.7103 A 0.455413
AFFX-LysX-5_at 6.37235 A 0.699394
AFFX-LysX-M_at 29.9084 A 0.250796
AFFX-LysX-3_at 1.51289 A 0.957052
AFFX-PheX-5_at 2.44236 A 0.963431
AFFX-PheX-M_at 5.76258 A 0.631573
AFFX-PheX-3_at 45.2136 A 0.440646
AFFX-ThrX-5_at 23.1458 A 0.147939
AFFX-ThrX-M_at 33.9437 A 0.123552

Total number of rows: 45101

Table truncated, full table size 1387 Kbytes.




Supplementary file Size Download File type/resource
GSM1639868_YLim-RHS-2_WTKSL-1a-Mouse430_2_Mouse430_2_.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM1639868_YLim-RHS-2_WTKSL-1a-Mouse430_2_Mouse430_2_.mas5.CHP.gz 395.1 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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