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Sample GSM2752394 Query DataSets for GSM2752394
Status Public on Mar 21, 2018
Title Control LPS-stimulated RAW264.7 cells Replicate1
Sample type RNA
 
Channel 1
Source name Control LPS-stimulated RAW264.7 cells
Organism Mus musculus
Characteristics cell line: RAW264.7
cell type: Macrophage-like
molecule: Sub-polysomal RNA
treatment: DMSO
Treatment protocol Cells were incubated with DMSO carrier or 125ng/ml mycolactone for 1hr then stimulated with 100ng/ml LPS for 4hr
Growth protocol RAW264.7 cells were grown in high glucose DMEM supplemented with 10% fetal bovine serum
Extracted molecule total RNA
Extraction protocol Cells treated with 10µg/ml cyclohexhamide for 10min and lysed in 15mM Tris pH7.4, 300mM NaCl, 15mM MgCl2, 100µg/ml cyclohexamide, 1mg/ml heparin. Polysomal and sub-polysomal RNA prepared by 10-60% sucrose gradient centrifugation and purified by LiCl precipitation
Label Cy3
Label protocol 0.15µg polysomal or subpolysomal RNA was spiked with Agilent RNA Spike-in Kit and labelled using Agilent Low input Quick Amp 2-colour labelling kit according to manufacturer's instructions
 
Channel 2
Source name Control LPS-stimulated RAW264.7 cells
Organism Mus musculus
Characteristics cell line: RAW264.7
cell type: Macrophage-like
molecule: Polysomal RNA
treatment: DMSO
Treatment protocol Cells were incubated with DMSO carrier or 125ng/ml mycolactone for 1hr then stimulated with 100ng/ml LPS for 4hr
Growth protocol RAW264.7 cells were grown in high glucose DMEM supplemented with 10% fetal bovine serum
Extracted molecule total RNA
Extraction protocol Cells treated with 10µg/ml cyclohexhamide for 10min and lysed in 15mM Tris pH7.4, 300mM NaCl, 15mM MgCl2, 100µg/ml cyclohexamide, 1mg/ml heparin. Polysomal and sub-polysomal RNA prepared by 10-60% sucrose gradient centrifugation and purified by LiCl precipitation
Label Cy5
Label protocol 0.15µg polysomal or subpolysomal RNA was spiked with Agilent RNA Spike-in Kit and labelled using Agilent Low input Quick Amp 2-colour labelling kit according to manufacturer's instructions
 
 
Hybridization protocol Pooled labelled cRNAs were fragemented at 60⁰C for 30min then applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After overnight hybridization at 65⁰C in Agilent Hi-RPM Hybridisation buffer, slides were washed according to manufacturer's instructions.
Scan protocol Scanned on an Agilent G2505C scanner
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
Description Biological replicate 1 of 3, DMSO treated, LPS stimulated RAW264.7 cells
Data processing Background correction by the normexp method; normalisation within arrays by Loess method and between arrays by Scale method; dyeswap correction; statistical analysis by RankProd method
 
Submission date Aug 23, 2017
Last update date Mar 21, 2018
Contact name RACHEL SIMMONDS
E-mail(s) rachel.simmonds@surrey.ac.uk
Phone 01483684714
Organization name University of Surrey
Street address FHMS UNIVERSITY OF SURREY, STAG HILL CAMPUS
City GULDFORD
State/province Surrey
ZIP/Postal code GU2 7XH
Country United Kingdom
 
Platform ID GPL10333
Series (1)
GSE103002 LPS stimulated murine RAW264.7 cells, incubated with DMSO carrier or mycolactone

Data table header descriptions
ID_REF
VALUE FC=mval(mycolactone+LPS)/mval(DMSO/LPS) where mval=mean values of polysomal fractions (n=3)/mean values of sub-polysomal fractions (n=3)

Data table
ID_REF VALUE
14570 -1.63156722
41204 -0.00527862
24697 -2.131893593
19759 -0.197704834
22852 0.26261313
31022 -2.522306277
6443 -0.598242705
7287 -2.50332316
20083 0.274512929
10483 -2.709740697
27761 -2.592732756
31001 -5.299526702
16288 -5.255588424
36984 -2.613543876
26483 -2.489310202
23961 -1.322015703
29374 -2.475369734
17983 -3.040277728
19967 -0.796059764
16903 -1.475290342

Total number of rows: 25519

Table truncated, full table size 452 Kbytes.




Supplementary file Size Download File type/resource
GSM2752394_RAW_-_A.txt.gz 4.2 Mb (ftp)(http) TXT
GSM2752394_RAW_-_A_dyeswap.txt.gz 4.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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