title: GSM2827718: HTT; Zea mays; Ustilago maydis; RNA-Seq
library_construction_protocol: One single infected/mock infected leaf was used per sample while three individual plants were analyzed per treatment/infective strain four days post infection.  14 µm transverse sections were cut at -20 °C using a cryostat (CM1900, Leica, Nussloch, Germany) microscopy glass slides. Tissue sections were immediately incubated in 50 % methanol for 1 min, followed by a methanol dehydration series (70 %, 1 min, 80 %, 1 min, 90 %, 1 min, 100 % methanol, 1 min), followed by 5 min immersion in xylene. Tissue sections were afterwards air-dried and subsequently used for LCM analysis. 1800-2000 cells were captured per sample using the PALM MicroBeam system (Zeiss, Jena, Germany) and adhesive caps (AdhesiveCap 200 opaque, Zeiss, Göttingen, Germany). For RNA extraction from dissected cells Arcturus® PicoPure® RNA isolation kit was used. Considering the very low amount of input material, we performed a pre-amplification using the Ovation® RNA Seq System V2 (NuGen, San Carlos, CA, USA).  2 ng of total RNA went in the generation of first strand cDNA using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement amplification. For library preparation we used the Illumina Nextera® XT DNA sample preparation protocol (Part # 15031942 Rev. C, Illumina, San Diego, CA, USA) starting with an input of 1 ng cDNA.
identifiers.namespace: GEO
identifiers.id: GSM2827718