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Sample GSM1009912 Query DataSets for GSM1009912
Status Public on Dec 24, 2013
Title Bone marrow macrophages 3 days CSF-1 versus 0 days ERT2 Cre Thoc5 (flox/flox) with tamoxifen rep2
Sample type RNA
 
Channel 1
Source name Bone marrow derived macrophages harvested at day 0 of differentiation induction
Organism Mus musculus
Characteristics cell type: Bone marrow macrophages
genotype: ERT2 Cre Thoc5 (flox/flox)
differentiation stage: day 0
treatment: none
genetic background: C57BL/6 x B6:129 Ola
Extracted molecule total RNA
Extraction protocol Cytoplasmic RNA was purified by use of the Pure RNA isolation Kit (Roth).
Label Alexa fluor 647
Label protocol Synthesis of Cy3- or Cy5-labeled cRNA was performed with the “Amino Allyl MessageAmp™ II aRNA Amplification Kit” (#5190-0444, Life Technologies) according to the manufacturer’s recommendations, except that the molar proportion of aminoallyl-UTP and UTP used was adjusted to 1+11 (instead of 1+1).
 
Channel 2
Source name Bone marrow derived macrophages harvested at day 3 after differentiation induction
Organism Mus musculus
Characteristics cell type: Bone marrow macrophages
genotype: ERT2 Cre Thoc5 (flox/flox)
differentiation stage: day 3 (under CSF-1)
treatment: tamoxifen
genetic background: C57BL/6 x B6:129 Ola
Extracted molecule total RNA
Extraction protocol Cytoplasmic RNA was purified by use of the Pure RNA isolation Kit (Roth).
Label Alexa fluor 555
Label protocol Synthesis of Cy3- or Cy5-labeled cRNA was performed with the “Amino Allyl MessageAmp™ II aRNA Amplification Kit” (#5190-0444, Life Technologies) according to the manufacturer’s recommendations, except that the molar proportion of aminoallyl-UTP and UTP used was adjusted to 1+11 (instead of 1+1).
 
 
Hybridization protocol cRNA fragmentation, hybridization and washing steps were carried-out exactly as recommended in the “Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7” (Agilent Technologies).
Scan protocol Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 5 µm, bit depth 20).
Data processing Data extraction, processing and intra-array normalization of raw fluorescence intensity values were performed with the “Feature Extraction Software V10.7.3.1” by using the recommended default extraction protocol file: GE2_107_Sep09.xml.
 
Submission date Sep 26, 2012
Last update date Dec 24, 2013
Contact name Oliver Dittrich-Breiholz
E-mail(s) dittrich.oliver@mh-hannover.de
Organization name Medical School Hannover
Department Research Core Unit Genomics
Street address Carl-Neuberg-Str. 1
City Hannover
ZIP/Postal code 30625
Country Germany
 
Platform ID GPL10333
Series (1)
GSE41170 THOC5, a member of the mRNA export complex, is essential for hematopoiesis in vivo and is required for CSF-1 induced macrophage differentiation

Data table header descriptions
ID_REF
VALUE Agilent defualt normalized log10 ratios (for experiment 1: Alexa647/Alexa555; for experiment 2: Alexa555/Alexa647) always representing: differentiation stage day 3 (under CSF-1) / diferentiation stage day 0.

Data table
ID_REF VALUE
1 0.061266802
2 0
3 0
4 0
5 0
6 0
7 0
8 0
9 0
10 0
11 0
12 0.020461274
13 0
14 0.540451029
15 -0.315908609
16 0.092051653
17 -0.075197595
18 0
19 0.248012688
20 0.33267159

Total number of rows: 44397

Table truncated, full table size 663 Kbytes.




Supplementary file Size Download File type/resource
GSM1009912_M3858-M3861_252665514368_S01_GE2_107_Sep09_1_4.txt.gz 15.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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