NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1160111 Query DataSets for GSM1160111
Status Public on Jun 01, 2016
Title PML-/- MEF 3h stimulation rep3
Sample type RNA
 
Source name PML-/- MEF 3h stimulation
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
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
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).
Label Cy3
Label protocol Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
 
Hybridization protocol Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.
Scan protocol Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
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.
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.).
 
Submission date Jun 11, 2013
Last update date Jun 01, 2016
Contact name Ruaidhri Carmody
E-mail(s) ruaidhri.carmody@glasgow.ac.uk
Organization name University of Glasgow
Department Institute of Infection, Immunity and Inflammation
Lab Room B/316
Street address Sir Graeme Davies Building, 120 University Place
City Glasgow
ZIP/Postal code G12 8TA
Country United Kingdom
 
Platform ID GPL15887
Series (1)
GSE47828 PML regulates NF-κB transcriptional activity

Data table header descriptions
ID_REF
VALUE RMA-normalized, averaged gene-level signal intensity

Data table
ID_REF VALUE
AB000096 946.86
AB000490 21.12
AB001425 247.91
AB001435 102.27
AB001539 10422.93
AB001750 3580.58
AB001926 8923.40
AB003502 11497.64
AB004048 142.37
AB005662 3322.64
AB005665 21.22
AB005909 18.28
AB006034 20.97
AB006103 19.56
AB007407 87.26
AB008928 58.88
AB009369 44.99
AB010088 18.96
AB010122 6796.82
AB011499 7174.21

Total number of rows: 44170

Table truncated, full table size 703 Kbytes.




Supplementary file Size Download File type/resource
GSM1160111_KO_TNF_3.pair.gz 2.3 Mb (ftp)(http) PAIR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.