2021-01-17
ENA first public
2021-01-07
ENA last update
ERC000011
ENA-CHECKLIST
SAMEA7769070
External Id
Insitute of Phytopathology, Justus Liebig University Gießen
INSDC center alias
Insitute of Phytopathology, Justus Liebig University Gießen
INSDC center name
2021-01-17T04:17:34Z
INSDC first public
2021-01-07T17:02:57Z
INSDC last update
public
INSDC status
ERS5516318
SRA accession
E-MTAB-9985:Sample 5
Submitter Id
3
week
age
ArrayExpress
http://www.ebi.ac.uk/efo/EFO_0009737
broker name
stiff brome
common name
Bd21-3
cultivar
Protocols: immediate freezing in liquid nitrogen Mo was grown on oatmeal agar (OMA) for two weeks at 26°C with 16 h light/8 h dark cycles both for sampling of mycelium and conidia production.For root inoculation, sterilized seeds (3% NaClO for 15 min, followed by three times 5 min washes in sterile water) of Bd21-3 were vernalized in the dark at 4°C for two days on half strength MS medium and then moved to a 16 h light (160 μmol m-2 s-1) /8 h dark cy-cle at 22°C/18°C. Roots of one-week-old seedlings were dip-inoculated in 1 ml of conidia solution (250,000 conidia/ml in 0.002% Tween water) for 3 h, transplanted in a (2:1) mix-ture of vermiculite (Deutsche Vermiculite GmbH) and Oil-Dri (Damolin, Mettmann, Ger-many) and grown for additional 4 days before harvesting. Control roots were mock-inoculated with 1 ml of Tween water solution. For leaf inoculation, third leaves of three-week-old Bd were detached and drop-inoculated with 10 μl of conidia solution (50,000 conidia/ml in 0.002% Tween water) on 1% agar plates. Control leaves were mock-inoculated with Tween water. Leaves were kept at 6 h light (160 μmol m-2 s-1) /8 h dark cycle at 22°C/18°C and collected for sequencing at 2 DPI (days post inoculation) and 4 DPI. Frozen tissue stored at -80°C was ground in liquid nitrogen using mortar and pestle. Total RNA was isolated with ZymoBIOMICS TM RNA Mini Kit (Zymo Research, USA). Quantity and integrity of the RNA were assessed with DropSense16/Xpose (BIOKÉ, Neth-erlands) and Bioanalyzer 2100 (Agilent, Germany), respectively. Purification of small and large RNAs into separate fractions was carried out using RNA Clean & Concentrator TM -5 (Zymo Research) and concentration and quality of the fractions were checked again, using the Agilent 2100 Bioanalyzer Pico Chip and the Qubit fluorometer (Invitrogen, Germany) for the sRNA fraction. 1.5 μg of large RNA were used for cDNA library preparation with TruSeq® Stranded mRNA (Illumina). Quality of polyA mRNA libraries was assessed using the Fragment Analyz-erTM Automated CE System (Advanced Analytical Technologies, Austria).
description
Brachypodium distachyon
http://purl.obolibrary.org/obo/NCBITaxon_15368
organism
Brachypodium distachyon
http://purl.obolibrary.org/obo/NCBITaxon_15368
organism
root
organism part
Sample 5
title