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Sample GSM541258 Query DataSets for GSM541258
Status Public on Oct 13, 2010
Title Wild type erythroblasts expressing ectopic Myc at supraphysiological levels 48hours 2
Sample type RNA
 
Source name E13.5 mouse fetal liver
Organism Mus musculus
Characteristics strain: C57BL/6
treatment: Infection with MSCV-c-Myc-IRES-GFP encoding retroviruses at 0 hours in culture, followed by FACS sorting for highly GFP positive cells at 48 hours post infection
genotype/variation: Myc at supraphysiological levels
time in culture: 48 hours
Treatment protocol Purified mouse fetal liver erythroblasts were cultured for 48 hours after infection with retroviruses encoding Myc or were cultured as uninfected cells for control.
Growth protocol Fetal livers were isolated from E13.5 C57BL/6 mice embryos and mechanically dissociated by pipetting in PBS containing 20% fetal bovine serum (FBS). The dissociated cells were passed through 70 and 30 micron strainers to obtain single-cell suspensions. The cells were labeled with magnetic microbead-conjugated antibodies for TER119 and CD11b and passed through LD columns according to the manufacturer’s instructions for negative selection (Miltenyi Biotec). The purified TER119-negative, CD11b-negative erythroid progenitor cells were seeded in fibronectin coated plates and cultured in Iscove’s modified Dulbecco medium (IMDM) containing 15% FBS, 1% detoxified bovine serum albumin (StemCell Technologies), 200 μg/mL holo-transferrin (Sigma),10 μg/mL recombinant human insulin (Sigma), 2 mM L-glutamine, 10-4 M β-mercaptoethanol, and 2 U/mL erythropoietin.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy Mini kit (Qiagen, Germany) according to manufacturer instructions. RNA quality was assessed on the 2100 Bioanalyser (Agilent, USA) using the RNA 6000 Nano Chip kit (Agilent, USA) for intact 18S and 28S ribosomal peaks without significant degradation (RNA Integrity Number >8) for all samples.
Label Biotin
Label protocol 500ng of total RNA from each sample was reverse transcribed into cDNA and in vitro transcribed into biotin-labelled cRNA using the Illumina TotalPrep RNA Amplification kit (Ambion, USA).
 
Hybridization protocol 750ng of each cRNA sample was hybridized to MouseRef-8 v2.0 Expression BeadChip microarrays (Illumina, USA) as per manufacturer specifications.
Scan protocol Microarrays were scanned on the BeadArray Reader (Illumina, USA) at scan factor 1 as per manufacturer specifications.
Description Biological replicate 2
D2 Myc-GFPhigh2
Data processing The microarray data was subjected to background subtraction and quantile normalization on the BeadStudio Data Analysis software (Illumina).
 
Submission date May 05, 2010
Last update date Oct 13, 2010
Contact name Senthil Raja Jayapal
E-mail(s) senthilraja@gis.a-star.edu.sg
Phone +65 64788187
Fax +65 6478-9005
Organization name Genome Institute of singapore
Department Stem cell and developmental biology
Lab Stem cell group 4
Street address #08-01, Genome, 60 Biopolis Street
City Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL6885
Series (1)
GSE18558 Downregulation of Myc is essential for terminal erythroid maturation

Data table header descriptions
ID_REF
VALUE Quantile-normalized signal intensity
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 1931.359 0
ILMN_2721178 464.9507 0
ILMN_3033922 337.3763 0
ILMN_3092673 1604.701 0
ILMN_2816356 25.53894 0
ILMN_2808939 644.5183 0
ILMN_2634564 394.906 0
ILMN_2737647 8.63728 0.1441558
ILMN_2734484 352.2074 0
ILMN_2952292 93.52248 0
ILMN_2699078 -4.781827 0.7038961
ILMN_1213681 141.8802 0
ILMN_2735413 -4.727379 0.7012987
ILMN_2735415 1.425928 0.4038961
ILMN_2891688 702.7342 0
ILMN_2637698 571.1384 0
ILMN_2674228 279.3377 0
ILMN_2601546 25.50175 0.001298701
ILMN_1230831 -3.720512 0.6324675
ILMN_2848071 12.85237 0.08181818

Total number of rows: 25697

Table truncated, full table size 732 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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