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Sample GSM2107289 Query DataSets for GSM2107289
Status Public on Aug 01, 2017
Title FG_RI3-4_C
Sample type RNA
 
Source name Infected_wheat_rachis3+4_7dpi
Organism Fusarium graminearum
Characteristics fusarium strain: PH-1
infection status: infected
wheat tissue: Rachis
Treatment protocol 200 Fusarium graminearum PH-1 conidia were incoluated into the floral caity of the two florets, of the two spikelets, in the middle of the wheat head at anthesis. Wheat plants were kept at high humidity for the first 3 days, of which the first 24 hours was in the dark. At 7 days post infection the incoluted spikelets and the 7 sequential rachis internodes below the inoculated spikelet were collected and immediately frozen in liquid nitrogen. The individual wheat tissues were pooled for ten wheat heads to form a single biological replicate. Non-infected wheat spikelets and rachis was collected as a negative control. Three biological replicate were collected per treatment.
Growth protocol Wheat plants were grown in a controlled environment with standard light, at 22 degrees and at ambient humidity
Extracted molecule total RNA
Extraction protocol Freeze dried samples were ground in liquid nitrogen with a pestle and mortar. Total RNA was extracted using the TRIzol® reagent (Invitrogen) with minor modifications to manufacturer’s instructions. Total RNA was precipitated at -20oC for 16 hours with 8 M lithium chloride.
Label biotin
Label protocol Purified total RNA (> 10 µg) was in vitro transcribed, labelled using the BioArray high yield RNA transcript labelling kit (T7) according to manufacturer’s instructions (Enzo Life Science)
 
Hybridization protocol Fragmented using 200 mM tris-acetate, pH 8.2, 500 mM MgOAc and mixed with the BioArray Eurkaryotic hydridization controls (Enzo Life Science) that included 3 nM control oligo B2, 20x control cRNA cocktail, herring sperma (10 mg / ml), acetylated BSA (50 mg / ml) 2x MES hybridization buffer and water. A final aRNA concentration of 10 µg in 200 µl was hybridized to the F. graminearum Affymetrix array
Scan protocol GeneChips were scanned using the GeneArray Scanner
Data processing Gene expression data from infecting hyphae within wheat floral tissue. The data was exported and RMA normalised using the Affymetrix Expression Console. Downstream analyses were performed with software R
 
Submission date Apr 02, 2016
Last update date Aug 01, 2017
Contact name Neil Brown
Organization name USP
Street address Av. do Cafe
City Ribeirao Preto
ZIP/Postal code 14040903
Country Brazil
 
Platform ID GPL18136
Series (1)
GSE79853 The biphasic Fusarium graminearum transcriptome during symptomless and symptomatic wheat infection

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
AFFX-BioB-5_at 9.113375
AFFX-BioB-M_at 9.254486
AFFX-BioB-3_at 9.133595
AFFX-BioC-5_at 9.994113
AFFX-BioC-3_at 9.984943
AFFX-BioDn-5_at 10.20435
AFFX-BioDn-3_at 12.74024
AFFX-CreX-5_at 13.69169
AFFX-CreX-3_at 13.92926
AFFX-DapX-5_at 3.586513
AFFX-DapX-M_at 3.669873
AFFX-DapX-3_at 3.91503
AFFX-LysX-5_at 3.415695
AFFX-LysX-M_at 5.079076
AFFX-LysX-3_at 3.476111
AFFX-PheX-5_at 4.17024
AFFX-PheX-M_at 3.569763
AFFX-PheX-3_at 5.508049
AFFX-ThrX-5_at 5.388579
AFFX-ThrX-M_at 4.03724

Total number of rows: 18069

Table truncated, full table size 394 Kbytes.




Supplementary file Size Download File type/resource
GSM2107289_018_PH1-RI1.2_R12_Fusariuma520094_.CEL.gz 2.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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