characteristics: ERC000011
characteristics: ENA-CHECKLIST
characteristics: 2022-10-27T14:00:27Z
characteristics: ENA-FIRST-PUBLIC
characteristics: 2022-10-27T14:00:27Z
characteristics: ENA-LAST-UPDATE
characteristics: SAMEA111452603
characteristics: External Id
characteristics: Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health,SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
characteristics: INSDC center name
characteristics: 2022-10-27T14:00:27Z
characteristics: INSDC first public
characteristics: 2022-10-27T14:00:27Z
characteristics: INSDC last update
characteristics: public
characteristics: INSDC status
characteristics: ERS13547149
characteristics: SRA accession
characteristics: E-MTAB-12261:Het_RNA
characteristics: Submitter Id
characteristics: ArrayExpress
characteristics: broker name
characteristics: Protocols: Sample for bulk RNA was collected by filtering 10 ml of culture in exponential phase (density of cells ≈ 10 mil) on 5 µm polycarbonate filters (Whatman).Filters were placed in cryoprotectant tubes with beads (Zirconium oxide beads, Precellys), amended with 600 µl of RLT buffer (Qiagen) which contained 1% of 2-Mercaptoethanol, shock frozen in liquid nitrogen and stored at -80 °C until further processing. For each cell type we collected samples for bulk RNA. Cells were harvested on 5 µm polycarbonate filters (Whatman). Filters were placed in cryoprotectant tubes with beads (Zirconium oxide beads, Precellys), amended with 600 µl of RLT buffer (Qiagen) which contained 1% of 2-Mercaptoethanol, shock frozen in liquid nitrogen and stored at -80 °C until further processing. Prior to RNA extraction, samples were taken out of -80, thawed on ice and subjected to bead beating (1x 6000 rmp, Precellys Evolution homogenizer). P. tricornutum and Heterocapsa sp. samples were treated for 2 min and T. thermophila just vortexed vigorously. RNA from samples was further extracted with the RNeasy Qiagen kit (QIAGEN, Inc., Valencia, CA) following the kit instructions. RNA was re-eluted in 30 µl of nuclease free water. Libraries were prepared with Magnatrix 8000+ (Nordiag), an eight-channel robotic workstation capable of running custom made scripts for in-tip magnetic bead separations41. Released mRNA-cDNA hybrids were transferred to the robotic workstation where they underwent second strand synthesis, end repair and in vitro transcription. Following transcription, sequencing adaptors are ligated to the RNA, and another round of cDNA synthesis is performed. Each step in the process is followed by a reaction clean-up step.
characteristics: description
characteristics: Heterocapsa sp.
characteristics: organism
characteristics: Heterocapsa sp.
characteristics: organism
characteristics: Heterocapsa sp.
characteristics: scientific_name
characteristics: non applicable
characteristics: spots with single cell detected
characteristics: CCAP 1125/4
characteristics: strain
characteristics: Het_RNA
characteristics: title