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Sample GSM1543923 Query DataSets for GSM1543923
Status Public on Jun 22, 2015
Title ΔnigR in glucose, biological rep2
Sample type RNA
 
Source name Streptococcus mutans UA159
Organism Streptococcus mutans UA159
Characteristics culture: planktonic cells
genotype: ΔnigR
Treatment protocol Cells were grown to the mid-log phase (OD600 = 0.65) and harvested by centrifugation.
Growth protocol Cells were grown in chemically-defined medium supplemented with 0.5% glucose.
Extracted molecule total RNA
Extraction protocol Cells were lysed using beat-beater. Extraction of total RNA was performed using Ambion RiboPure Bacteria kit according to the manufacturers protocol.
Label biotin
Label protocol Biotinylated cDNA was prepared according to the standard Affymetrix protocol.
 
Hybridization protocol Following fragmentation, 3 μg of cDNA were hybridized for 16 hr at 47℃ on GeneChip S. mutans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using a laser scanner 7G (Affymetrix)
Description Gene transcription data from planktonic culture OD600=0.65
Data processing Data was analyzed with Expression and Transcription Analysis Console software from Affymetrix using default analysis settings and global scaling as normalization method.
 
Submission date Nov 12, 2014
Last update date Jun 22, 2015
Contact name Dragana Ajdic
E-mail(s) [email protected]
Phone 305-243-0475
Organization name University of Miami
Department Dermatology
Street address 1600 NW 10th Ave, RMSB 2023
City Miami
State/province Florid
ZIP/Postal code 33136
Country USA
 
Platform ID GPL4769
Series (1)
GSE63213 Regulation of PTSBio by transcriptional repressor NigR

Data table header descriptions
ID_REF
VALUE MAS5
Detection
Detection p-value

Data table
ID_REF VALUE Detection Detection p-value
SMU_01_at 1068.386597 P 0.000147
SMU_02_at 1254.061523 P 0.000147
SMU_05_at 403.163116 P 0.000147
SMU_06_at 1242.176758 P 0.000176
SMU_07_at 721.952759 P 0.000147
SMU_08_at 686.68634 P 0.000147
SMU_09_at 1091.516357 P 0.000147
SMU_10_at 1177.790894 P 0.000147
SMU_11_at 979.981017 P 0.000147
SMU_12_at 1126.228638 P 0.000147
SMU_13_at 763.725647 P 0.000147
SMU_14_at 1531.578491 P 0.000147
SMU_15_at 1755.171143 P 0.000147
SMU_16_at 747.068726 P 0.000147
SMU_18_at 327.058258 P 0.000147
SMU_18_s_at 1871.986572 P 0.000147
SMU_20_at 912.507874 P 0.000147
SMU_21_at 677.009827 P 0.000147
SMU_22_at 1685.61438 P 0.000147
SMU_23_at 1190.450195 P 0.000147

Total number of rows: 1912

Table truncated, full table size 64 Kbytes.




Supplementary file Size Download File type/resource
GSM1543923_nigR_glu2_11032014.CEL.gz 544.3 Kb (ftp)(http) CEL
GSM1543923_nigR_glu2_11032014.mas5.CHP.gz 41.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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