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Sample GSM3146148 Query DataSets for GSM3146148
Status Public on Jul 12, 2018
Title BM_CONTROL_REP1
Sample type RNA
 
Source name bone marrow, control
Organism Homo sapiens
Characteristics tissue: Bone Marrow
treatment: Control
Treatment protocol Mice were dosed twice a day with 2 mg/kg PI3Kd
Growth protocol NALM6 cells were engrated in SCID mice, which were treated with control/PI3Kd until animals reached clinical endpoint.
Extracted molecule total RNA
Extraction protocol Mouse femurs were collected and BM cells were aspirated with RPMI1640 containing 10% FBS. Murine spleen tissues were homogenized in RPMI1640 containing 10% FBS. The spine was removed from mice, cut into columns and aspirated with RPMI1640 containing 10% FBS to collect CSF cells. The BM, spleen and CSF cells were passed through 70 μm filters, washed with PBS and treated with ACK lysis buffer.RNA was extracted using RNAeasy kit (Qiagen, Germantown, MD) and total RNA were assessed for quality with Agilent 2100 Bioanalyzer G2939A (Agilent Technologies,Santa Clara, CA) and Nanodrop 8000 spectrophotometer (Thermo Scientific/Nanodrop, Wilmington, DE).
Label biotin
Label protocol Affymetrix WT Plus Kit (PN 902280) and GeneChip WT Terminal Labeling Kit (PN 900670)
 
Hybridization protocol Hybridization targets were prepared with the Affymetrix WT Plus Kit (Affymetrix, Santa Clara, CA) and Affymetrix GeneChip WT Terminal Labeling Kit (included with Affy WT Plus) from total RNA, hybridized to GeneChip® Human Clariom D arrays in Affymetrix GeneChip® hybridization oven 645, washed in Affymetrix GeneChip® Fluidics Station 450 and scanned with Affymetrix GeneChip® Scanner 7G according to standard Affymetrix GeneChip® Hybridization, Wash, and Stain protocols. (Affymetrix, Santa Clara,CA).
Scan protocol Affymetrix scanning protocol according to manufacturer, Affymetrix GeneChip Command Console Scan Control 3.2.3.1515 and Expression Console version 1.2.0.20
Description NALM6 human ALL cells isolated from SCID mice after control/PI3Kd treatment
Data processing Total RNA isolated from BM and CSF was sent for gene expression profiling using the Clariom D Human microarrays (Affymetrix, Santa Clara, USA) at the Duke Center for Genomic and Computational Biology. Raw cell intensity data was imported in to Expression Console (Affymetrix, Santa Clara, USA) and BM arrays (vehicle and GS-649443 samples), and CSF arrays (vehicle and GS-649443) were normalized using the RMA algorithm. Gene level differential expression analysis was performed using the Transcript Analysis Console (v3.1.0.5: Affymetrix, Santa Clara, USA) and ANOVA statistical analysis performed on the BM and CSF arrays separately. Transcripts identified to be differentially regulated in the BM, or CSF samples by ±1.5-fold with a p-value <0.05 were carried forward for pathway analysis.
 
Submission date May 18, 2018
Last update date Jul 12, 2018
Contact name Dorothy Sipkins
Organization name Duke University
Department Hematological Malignancies and Cell Therapy
Lab Sipkins Lab
Street address 905S La Salle Street
City Durham
State/province NC
ZIP/Postal code 27710
Country USA
 
Platform ID GPL23126
Series (1)
GSE114627 Leukemia hijacks a neural mechanism to invade the central nervous system

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AFFX-BkGr-GC03_st 1.940896
AFFX-BkGr-GC04_st 1.961071
AFFX-BkGr-GC05_st 1.981148
AFFX-BkGr-GC06_st 2.059854
AFFX-BkGr-GC07_st 2.064981
AFFX-BkGr-GC08_st 2.125798
AFFX-BkGr-GC09_st 2.203042
AFFX-BkGr-GC10_st 2.291061
AFFX-BkGr-GC11_st 2.506961
AFFX-BkGr-GC12_st 2.777898
AFFX-BkGr-GC13_st 3.280055
AFFX-BkGr-GC14_st 3.778313
AFFX-BkGr-GC15_st 4.344296
AFFX-BkGr-GC16_st 5.255389
AFFX-BkGr-GC17_st 5.565902
AFFX-BkGr-GC18_st 6.193236
AFFX-BkGr-GC19_st 6.648062
AFFX-BkGr-GC20_st 6.994916
AFFX-BkGr-GC21_st 7.182797
AFFX-BkGr-GC22_st 7.714949

Total number of rows: 138745

Table truncated, full table size 3668 Kbytes.




Supplementary file Size Download File type/resource
GSM3146148_4580_16923_46759_MW1_ClariomDHuman.CEL.gz 25.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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