Project description:Seven closely related species from Hologalegina and Phaseoloid clades were selected: Lathyrus sativus, Pisum sativum (Lathyrus oleraceus), Lens culinaris, Cicer arietinum, Medicago truncatula, Glycine max, and Phaseolus vulgaris, to assess tissue-specific expression in non-inoculated conditions. Plants were cultivated in 0.5 L pots containing growth medium (50% soil, 25% vermiculite, 25% peat) in controlled environment chambers at 22°C with a 12/12-hour photoperiod. At the three fully expanded leaf developmental stage, leaf and root tissues were harvested separately, and RNA was extracted. RNA samples were submitted for Illumina NovaSeq 6000 Sequencing PE150 (40 million paired-end reads per sample) at Novogene (UK) Co. Raw reads were trimmed with cutadapt and gene counts were obtained using StringTie with the respective annotation files of each genome.
Project description:jc2013_sybiopop_2014-pilot transcriptomic study - Which genes affect biomass yield in poplar? RNA was extracted from young differentiating xylem and cambium collected on 24 4-year-old trees trialed in a common garden experiment at INRA Orléans. The trees corresponded to corresponding to 2 replicates of 12 genotypes from 6 natural populations. After RNA quantification, the RNA from xylem and cambium from the same tree were pooled and subjected to high-throughput sequencing on an Illumina HiSeq 2000 using 100 bp paired-ends reads indexing runs. All the samples were sequenced on one Illumina lane, yielding around 20 million of single-reads per sample.
Project description:RNA sequencing was performed to investigate the transcriptomic response of Dunaliella salina cultivated in Sistan deep water. Four RNA-seq libraries representing two biological replicates for the control and two biological replicates for the deep water treatment were generated using the Illumina NovaSeq 6000 platform. Raw sequencing data are available in SRA under BioProject PRJNA1267574. Processed gene count data are provided.
Project description:ChIP-seq was performed to profile H4R3me2a occupancy in HCT116 colorectal cancer cells with matched input DNA control. Libraries were sequenced as paired-end 150 bp reads on an Illumina NovaSeq 6000. Reads were aligned to GRCh38 with Bowtie2, peaks were called with MACS2 (q < 0.05), and metagene profiles were generated with deepTools.
Project description:Candida parapsilosis CLIB 214 (CBS 604) was grown on synthetic media containing hydroxyaromatic compounds as a sole carbon source. The cells cultivated in medium containing galactose were used as a control. Total RNA was isolated using hot acid phenol extraction. A TruSeq stranded mRNA library was sequenced on an Illumina NovaSeq 6000 system.
