NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1303893 Query DataSets for GSM1303893
Status Public on Jul 23, 2014
Title dsho1dmsb2 Parafilm 12h, biological rep3
Sample type RNA
 
Source name U. maydis AM1dsho1dmsb2 culture sprayed on parafilm surface
Organism Mycosarcoma maydis
Characteristics cellular differentiation: filamentous cells
genotype: AM1Δsho1Δmsb2
time: 12 h
treatment: incubated for 12h on hydrophobic surface
Treatment protocol Cell suspensions were sprayed on glass or Parafilm; droplet size on Parafilm did not exceed 2 mm
Growth protocol Ustilago maydis strains were grown to mid-log phase (OD600 of 0.8) in liquid YEPSL medium and resuspended in 2% YEPSL (OD600 of 1.0) supplemented with or without 100 uM 16-hydroxy hexadecanoic acid (HDA).
Extracted molecule total RNA
Extraction protocol Cells were harvested from the surfaces using a cell scraper and total RNA was extracted with Aquaphenol/Chloroform.
Label Biotin
Label protocol Biotinylated aRNA was prepared from 100 ng total RNA using the GeneChip 3’ IVT Express Kit (Affymetrix)
 
Hybridization protocol 15 ug of fragmented aRNA were hybridized on GeneChip UstilagoA custom arrays and washed with Affymetrix protocols (GeneChip Hybridization Wash and Stain Kit; Midi_Euk2V3 protocol on GeneChip Fluidics Station 450)
Scan protocol GeneChips were scanned using Affymetrix GSC3000G
Description Gene expression data from U. maydis sho1 msb2 double deletion mutant incubated for 12 on hydrophobic surface
Data processing Data was analyzed with GCOS (Affymetrix Microarray Suite 5.9) to create CEL files. Data was normalized with the RMA method using Partek Genomics Suite 6.5
 
Submission date Jan 09, 2014
Last update date Jul 23, 2014
Contact name Regine Kahmann
E-mail(s) [email protected]
Organization name MPI for Terrestrial Microbiology
Department Organismic Interactions
Lab Kahmann
Street address Karl-von-Frisch Str. 10
City Marburg
ZIP/Postal code 35043
Country Germany
 
Platform ID GPL3681
Series (1)
GSE53947 Ustilago maydis gene expression after growth on hydrophobic surface plus/minus hydroxy fatty acids

Data table header descriptions
ID_REF
VALUE RMA signal intensity

Data table
ID_REF VALUE
AFFX-BioB-3_at 5.12919
AFFX-BioB-5_at 6.0467
AFFX-BioB-M_at 5.75559
AFFX-BioC-3_at 6.84495
AFFX-BioC-5_at 7.15791
AFFX-BioDn-3_at 9.86545
AFFX-BioDn-5_at 7.76148
AFFX-CreX-3_at 12.28236
AFFX-CreX-5_at 10.97431
AFFX-DapX-3_at 3.67096
AFFX-DapX-5_at 3.50536
AFFX-DapX-M_at 3.60224
AFFX-LysX-3_at 3.59029
AFFX-LysX-5_at 3.33841
AFFX-LysX-M_at 3.91238
AFFX-PheX-3_at 4.8066
AFFX-PheX-5_at 3.27635
AFFX-PheX-M_at 3.53609
AFFX-ThrX-3_at 4.51917
AFFX-ThrX-5_at 4.15598

Total number of rows: 6795

Table truncated, full table size 142 Kbytes.




Supplementary file Size Download File type/resource
GSM1303893_DLPB_12h_ParafilmIII_SG200dsho1dmsb2.CEL.gz 2.1 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap