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Sample GSM2051824 Query DataSets for GSM2051824
Status Public on Feb 19, 2016
Title strain CV571, mock treatment, rep 1
Sample type RNA
 
Source name Enterococcus faecium
Organism Enterococcus faecium
Characteristics sample: Whole cell
strain: CV571 (pbfF ponA)
agent: Mock
growth phase: exponential phase
Treatment protocol An equal volume of ice cold acetone:ethanol (1:1) was added to inactivate bacterial ribonucleases
Growth protocol E. faecium strain CV571 (pbfF ponA) was grown to mid-exponential phase (Optical Density 600nm of 0.4 to 0.5) in Brain-Heart Infusion broth at 37C with aeration (200 rpm in a rotary shaker). Cells were then continued to grow for 30 min during either: 1. mock conditions (37C at 200 rpm in an orbital shaker) or 2. penicillin challenge conditions (10 micrograms per milliliter; 37C at 200 rpm in an orbital shaker).
Extracted molecule total RNA
Extraction protocol Culture samples were mechanically disrupted in a Biospec Beadbeater using 0.5 mm RNase-free zirconium oxide beads. Following disruption, total bacterial RNA was purified using a Qiagen Rneasy Mini kit.
Label Biotin
Label protocol 10 micrograms of each sample was labeled per Affymetrix (Santa Clara, CA) instructions for prokaryotic arrays (reverse transcribed, DNase I fragmentation and 3' biotinylated).
 
Hybridization protocol 1.5 ug of RNA were hybrized for 16 hr at 45C on an E. faecium Affymetrix GeneChip. GeneChips were washed and stained in an Affymetrix Fluidics Station using ProKaryotic GE-wash2 protocol.
Scan protocol GeneChips were scanned in an Affymetrix 7G GeneArray Scanner
Description Gene expression data from mock treated E. faecium strain CV571
Data processing The data were analyzed with Microarray Suite version 5.0 using Affymetrix default analysis settings.
 
Submission date Feb 01, 2016
Last update date Feb 19, 2016
Contact name Paul Dunman
E-mail(s) paul_dunman@urmc.rochester.edu
Phone 585-276-5700
Organization name University of Rochester
Department Microbiology and Immunology
Street address 601 Elmwood Avenue
City Rochester
State/province NY
ZIP/Postal code 14642
Country USA
 
Platform ID GPL21391
Series (1)
GSE77436 Emergence of cephalosporin resitance in cephalosporin-sensitive class A penicillin binding protein mutants in Enterococcus faecium

Data table header descriptions
ID_REF
VALUE MAS5 signal
DetectionPValue

Data table
ID_REF VALUE DetectionPValue
gi-EFXG_00008T0_at 7.80108 0.691895
gi-EFXG_00008T0_s_at 1761.503418 0.000244
gi-EFXG_00040T0_at 1.058434 0.822754
gi-EFXG_00041T0_at 1.409813 0.969727
gi-EFXG_00042T0_at 18.486366 0.559082
gi-EFXG_00043T0_at 22.509045 0.27417
gi-EFXG_00044T0_at 1.852342 0.904785
gi-EFXG_00045T0_at 1.102257 0.884033
gi-EFXG_00049T0_at 35.074024 0.007568
gi-EFXG_00086T0_s_at 4046.828857 0.000244
gi-EFXG_00101T0_at 4655.89209 0.000244
gi-EFXG_00138T0_at 13.188214 0.601074
gi-EFXG_00138T0_s_at 153.889206 0.018555
gi-EFXG_00139T0_s_at 46.58477 0.008057
gi-EFXG_00141T0_at 19.741465 0.466064
gi-EFXG_00141T0_s_at 939.912781 0.000244
gi-EFXG_00143T0_s_at 139.750549 0.000244
gi-EFXG_00168T0_s_at 2025.565674 0.000244
gi-EFXG_00190T0_at 148.537689 0.023926
gi-EFXG_00192T0_at 2.748414 0.960449

Total number of rows: 4395

Table truncated, full table size 167 Kbytes.




Supplementary file Size Download File type/resource
GSM2051824_2014_05_02_E._faecium_CV571_N1_PMDefcma520788F_.2014_05_02_E._faecium_CV571_N2.mas5.CHP.gz 28.9 Kb (ftp)(http) CHP
GSM2051824_2014_05_02_E._faecium_CV571_N1_PMDefcma520788F_.CEL.gz 363.4 Kb (ftp)(http) CEL
Processed data included within Sample table
Processed data provided as supplementary file

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