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Sample GSM679696 Query DataSets for GSM679696
Status Public on Oct 05, 2011
Title Bone marrow transduced with MIG, biological replicate-2
Sample type RNA
 
Source name Adult mouse bone marrow
Organism Mus musculus
Characteristics strain: C57/BL6/C3H
cell type: bone marrow cells
transducer: MIG
Treatment protocol After 48 hours of pre-stimulation, the BM cells were transduced with different viruses, containing the relevent constructs, by overlaying them on virus-producing irradiated (40 Gy) GFP+E86 producers in the presence of cytokines and protamine sulfate (5ug/ml). The transduction was stopped by removing the BM cells from the GFP+E86 cells and plating them in BM medium with cytokines for another 48 hours to allow for GFP expression. Retrovirally transduced cells were FACS sorted based on expression of GFP.
Growth protocol Adult C57/BL6/C3H mice were injected with 30µg/µl working solution of 5-Fluorouracil (100µl per 20gr of weight) to enrich for stem and progenitor cells. Four days post injection, total bone marrow
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from FACS sorted GFP+ cells using the Qiagen miRNeasy Mini Kit For purification of microRNA and total RNA from tissues and cells per manufacturer's instructions
Label biotin
Label protocol Samples were labeled using the FlashTag™ Biotin HSR Kit from Genisphere starting with 1µg of totel RNA according to the protocol of the manufaturer
 
Hybridization protocol accoring to the recommended protocol followed by washing at a Fluidics Station 450 using fluidics script FS450_0003
Scan protocol according to Affymetrix protocols using a GeneChip 3000 Scanner
Description Gene expression data from bone marrow cells 96 hours post-transdution with MIG
Data processing Data were processed using the miRNAQC tool from Affymetrix following the recommended workflow from Genisphere (Background Detection -> RMA Global Background Correction -> Quantile Normalization -> Median polish Summarization); Statistical analysis was done using BRB Array-Tools Software by Richard Simon
 
Submission date Feb 24, 2011
Last update date Oct 05, 2011
Contact name Karlheinz Holzmann
E-mail(s) karlheinz.holzmann@uni-ulm.de
Organization name Ulm University
Department Medical Faculty
Lab Genomics Core Facility
Street address Helmholtzstreet 8/1
City Ulm
ZIP/Postal code D-89081
Country Germany
 
Platform ID GPL8786
Series (2)
GSE27512 Identification of a Potently Oncogenic CALM-AF10 Minimal-Fusion Mutant (miRNA)
GSE27514 Identification of a Potently Oncogenic CALM-AF10 Minimal-Fusion Mutant

Data table header descriptions
ID_REF
VALUE Quantile normalized, log2

Data table
ID_REF VALUE
ACA59_s_st 0.4366782
ACA35_st -0.1664385
U17a_st 0.1131757
U17a_x_st 0.413377
U17b_st 4.138828
U17b_x_st 1.805714
HBII-420_st 0.7133823
ACA61_st 0.5527969
ACA44_st 1.047501
ACA16_st 0.4744171
ACA16_x_st 0.03591985
U103_s_st -0.09797081
HBII-251_st 0.4440671
ACA55_st 0.5247848
U55_st 0.2760035
U55_x_st 0.924017
U46_st 0.1400048
U46_x_st 0.7489359
U38A_st 0.2042307
U38B_st 0.1374803

Total number of rows: 7625

Table truncated, full table size 190 Kbytes.




Supplementary file Size Download File type/resource
GSM679696.CEL.gz 141.9 Kb (ftp)(http) CEL
Processed data included within Sample table

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