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Status |
Public on Jun 01, 2016 |
Title |
PML-/- MEF 3h stimulation rep3 |
Sample type |
RNA |
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Source name |
PML-/- MEF 3h stimulation
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Organism |
Mus musculus |
Characteristics |
strain background: C57/B6 genotype/variation: PML-/- cell type: mouse embryonic fibroblasts (MEFs) stimulated with: 10ng/ul mouse TNFα for 3hrs
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Growth protocol |
WT MEFs, PML -/- MEFs cells were maintained in tissue culture dishes and/or flasks (Iwaki) in Dulbecco’s modified eagle medium (DMEM) at 37˚C, 5% CO₂. Cell maintenance medium was as follows: 500ml DMEM (GIBCO; 41966), 10% v/v foetal bovine serum (FBS;), 5ml 1,000U/ml penicillin-streptomycin (Invitrogen), 5ml Glycine (Sigma) Cells were treated with a final concentration of 10ng/ul mouse TNFα for 3 hours
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using the RNeasy Mini kit (Qiagen Inc., Valencia, CA, USA) and the RNAprotect reagent (Qiagen) and DNA was removed by on-column DNase digestion with the RNase-Free DNase set (Qiagen). RNA quality and concentration was determined by analysis with an Agilent 2100 bioanalyzer at the Harvard-Partners Center for Genetics and Genomics (Harvard Medical School, Cambridge, MA USA).
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Label |
Cy3
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Label protocol |
Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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Hybridization protocol |
Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
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Scan protocol |
Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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Description |
KO TNF 3 This sample is of PML knockout mouse embryonic fibroblasts treated with TNFalpha for 3 hours. It is the third of three TNFalpha treated PML knockout biological replicates used in this experiment, each from separate cultures.
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Data processing |
The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.).
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Submission date |
Jun 11, 2013 |
Last update date |
Jun 01, 2016 |
Contact name |
Ruaidhri Carmody |
E-mail(s) |
ruaidhri.carmody@glasgow.ac.uk
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Organization name |
University of Glasgow
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Department |
Institute of Infection, Immunity and Inflammation
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Lab |
Room B/316
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Street address |
Sir Graeme Davies Building, 120 University Place
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City |
Glasgow |
ZIP/Postal code |
G12 8TA |
Country |
United Kingdom |
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Platform ID |
GPL15887 |
Series (1) |
GSE47828 |
PML regulates NF-κB transcriptional activity |
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