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Status |
Public on Sep 14, 2012 |
Title |
adult_KSL-HLX_expression_vector-2 |
Sample type |
RNA |
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Source name |
Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow infected with mouse HLX (pCAD-HLX-IRES-GFP) lentivirus, cultured for 2 days, then sorted for GFP+ cells
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Organism |
Mus musculus |
Characteristics |
vector: HLX cell type: infected, GFP+, sorted adult bone marrow Lin-Kit+Sca-1+ cells age: young adult strain: FVB/nJ
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Treatment protocol |
Sorted Lin-Kit+Sca-1+ cells from young adult wild-type FVB/nJ bone marrow were infected with control (pCAD-IRES-GFP) or Hlx lentivirus (pCAD-IRES-GFP-Hlx) in in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF in the presence of 8ug/ml polybrene. GFP-positive cells were sorted 2 days after transduction.
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Growth protocol |
Cells were cultured in Iscove’s modified Dulbecco’s medium (IMDM) containing FBS, mIL-3, mIL-6 and mSCF.
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Extracted molecule |
total RNA |
Extraction protocol |
GFP-positive cells were sorted 2days after transduction by FACS and RNA was extracted from 5,000 to 10,000 GFP-positive cells using the RNeasy Micro Kit (Qiagen).
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Label |
biotin
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Label protocol |
3ng RNA was used for amplification of cDNA by Nugen Ovation pico WTA system following the manufacture’s protocol. labeling was performed by GeneChip WT terminal labeling kit (Affymetrix).
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Hybridization protocol |
Hybridization kit; GeneChip Hybridization Wash and Stain Kit (Affymetrix). GeneChip; Affymetrix Mouse Gene 1.0ST microarrays (Affymetrix)
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Scan protocol |
GeneChip Scanner 3000 7G system (Affymetrix).
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Description |
Sorted Lin-Kit+Sca-1+ cells from wild-type FVB/nJ bone marrow infected with mouse HLX (pCAD-HLX-IRES-GFP) lentivirus, cultured for 2 days, then sorted for GFP+ cells
|
Data processing |
Microarray data was normalized with the RMA algorithm of Affymetrix Power Tools (v 1.178). Log2-transformed signals are listed. A t-test with Welch approximation for unequal group variances with p-values based on t-distribution was performed with a cutoff of p<0.1 in Multiple Experiment Viewer v.4 pilot2 (http://www.tm4.org/mev/) (PMID: 16939790). Subsequently, the probes with -log10(p) value <0.05 and a mean difference > 0.5 were considered differentially expressed and used for further analysis.
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Submission date |
Mar 14, 2011 |
Last update date |
Sep 14, 2012 |
Contact name |
Boris Bartholdy |
Organization name |
Albert Einstein College of Medicine
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Department |
Cell Biology
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Street address |
1300 Morris Park Ave
|
City |
Bronx |
State/province |
NY |
ZIP/Postal code |
10461 |
Country |
USA |
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Platform ID |
GPL6246 |
Series (2) |
GSE27938 |
Identification of differentially regulated genes upon overexpression of HLX in wild-type hematopoietic stem cells |
GSE27947 |
Identification of differentially regulated genes in hematopoietic stem cells and URE leukemia cell line |
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