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Sample GSM1516134 Query DataSets for GSM1516134
Status Public on Dec 17, 2015
Title BMDM-baseline-rep1
Sample type RNA
 
Source name bone marrow derived macrophage
Organism Mus musculus
Characteristics gender: male
cell type: bone marrow derived macrophage
time: baseline
treatment: baseline
Treatment protocol Samples were treated with 100nM dexamethasone (Sigma) for the indicated duration
Growth protocol Bone marrow from 3 10 week old male C57BL/6 was extracted and differentiated in culture with 10% fetal calf serum and recombinant human CSF1 (10,000U/ml) for 1 week. They were then replated, again with serum and rhCSF1, at 0.5M cells/ml frot he time series.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the RNeasy kit (Qiagen) and quality assessed using an 2100 Bioanalyzer (Agilent )
Label biotin
Label protocol Standard affymetrix protocols, Performed by Edinburgh Genomics.
 
Hybridization protocol Standard affymetrix protocols using GeneTitan. Performed by Edinburgh Genomics.
Scan protocol Standard affymetrix protocols using GeneTitan. Performed by Edinburgh Genomics.
Description 10week old
Data processing Raw data was processed using R/Bioconductor: arrayQualityMetrics for quality control and the rma algorithm in the affy package to generate expression values.
 
Submission date Sep 29, 2014
Last update date Dec 17, 2015
Contact name Alasdair W Jubb
E-mail(s) alasdair.jubb@ed.ac.uk
Organization name University of Edinburgh
Department Roslin Institute
Lab Hume lab / Bickmore lab (MRC HGU)
Street address The Roslin Institute
City Easter Bush
State/province Midlothian
ZIP/Postal code EH25 9RG
Country United Kingdom
 
Platform ID GPL11180
Series (2)
GSE61879 Expression data from a 24h time series of dexamethasone treatment for mouse bone marrow derived macrophages
GSE61881 Divergent transcriptional activation by glucocorticoids in mouse and human macrophages is the result of gain and loss of enhancers

Data table header descriptions
ID_REF
VALUE unlogged rma signal

Data table
ID_REF VALUE
1419783_PM_at 7.001669467
1419784_PM_x_at 11.24954288
1419785_PM_at 8.291250829
1419790_PM_at 19.46693555
1419793_PM_at 7.836253511
1419801_PM_x_at 10.660602
1419822_PM_at 8.158767502
1419830_PM_at 8.938288195
1419836_PM_at 18.81195515
1419859_PM_at 6.888220329
1419861_PM_at 7.186958553
1419863_PM_at 10.66389816
1419881_PM_x_at 8.486822511
1419956_PM_at 8.527662207
1419957_PM_at 8.981043025
1419990_PM_at 10.6216127
1419991_PM_at 6.958757645
1419992_PM_x_at 7.027391865
1419993_PM_at 8.700927987
1420001_PM_at 9.920969163

Total number of rows: 45141

Table truncated, full table size 1159 Kbytes.




Supplementary file Size Download File type/resource
GSM1516134_M1_0.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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