Project description:The douple mutant Arabidopsis thaliana soc1 ful, in contrast with WT, produces an interfascicular cambium and a large wood cylinder is the flowering stem. We present the RNAseq data for polyA mRNA of different developmental stages of cambium and wood formation in Arabidopsis thaliana. We sequenced 7 stages; 4 in the woody mutant soc1-6 ful-7 (herbaceous, cambium initiation, wood initiation and leaf) and 3 stages in the WT Col-0 (herbaceous, cambium and leaf). The corresponding stem anatomy is also presented in the manuscript indicating the stage of cambium development and the production of secondary xylem.
Project description:MicroRNAs (miRNAs) are small noncoding regulatory RNAs that play key roles in the process of plant development. To date, extensive studies of miRNAs have been performed in a few model plants, but few efforts have focused on small RNAs in conifers because of the lack of reference sequences for these enormous genomes. In this study, Solexa sequencing of three small RNA libraries obtained from dormant, reactivating, and active vascular cambium in Chinese fir samples identified 76 known miRNAs from 27 miRNA families and 18 new potential miRNAs, of which 15 novel miRNA precursors were validated by RT-PCR and sequencing. More than half of these novel miRNAs displayed stage-specific expression patterns in the vascular cambium. Furthermore, analyzing the 103 miRNAs and their predicted targets indicated that 30% of miRNAs appeared to negatively regulate their targets, of which 4 target genes involved in the regulation of cambial cell division were validated via RNA ligase-mediated rapid amplification of 5’ cDNA ends (RLM 5’-RACE). Interestingly, miRNA156 and miRNA172 may regulate the phase transition in vascular cambium from dormancy to active growth. These results provide new insights into the important regulatory functions of miRNAs in vascular cambium development and wood formation in conifers.
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:Comparison of small RNA fractions derived from piRNA clusters and transposon sequences in control and Su(var)3-7 null mutant. Small RNA profile of 3-day old control and Su(var)3-7 mutant ovaries were generated by high-throughput sequencing on Illumina HiSeq 2000
Project description:The barley R gene (Mla6aa1-161) dataset was part of a larger Y2H screen (GEO GSE150396) to identify novel proteins involved in barley immune responses. Yeast-two-hybrid (Y2H) screening was coupled with next-generation sequencing to identify and quantify interacting proteins. The Mla6aa1-161 bait was mated to a cDNA prey library derived from a 0-48 hour time course of infected leaf tissue. Screens were performed in batch liquid culture to enrich yeast populations for cells expressing positive interactions. After two rounds of enrichment under selective (Histidine absent) and non-selective (Histidine present) conditions, yeast cells were collected. Y2H plasmids were extracted and prey cDNA amplicons were generated via low-cycle PCR. Fragmented amplicons were used as input to generate sequencing libraries and processed on the HiSeq 3000 platform. Reads were mapped to the barley and Blumeria graminis genomes and read counts were analyzed using a custom data processing and scoring pipeline. Putative interactors were cloned and binary Y2H was used to confirm interactions.
Project description:The barley powdery mildew effector (CSEP0491) dataset was part of a larger Y2H screen (GEO GSE150396) to identify novel proteins involved in barley immune responses. Yeast-two-hybrid (Y2H) screening was coupled with next-generation sequencing to identify and quantify interacting proteins. The CSEP0491 bait was mated to a cDNA prey library derived from a 0-48 hour time course of infected leaf tissue. Screens were performed in batch liquid culture to enrich yeast populations for cells expressing positive interactions. After two rounds of enrichment under selective (Histidine absent) and non-selective (Histidine present) conditions, yeast cells were collected. Y2H plasmids were extracted and prey cDNA amplicons were generated via low-cycle PCR. Fragmented amplicons were used as input to generate sequencing libraries and processed on the HiSeq 3000 platform. Reads were mapped to the barley and Blumeria graminis genomes and read counts were analyzed using a custom data processing and scoring pipeline. Putative interactors were cloned and binary Y2H was used to confirm interactions.
Project description:The barley powdery mildew avirulence effector (AVRA1) dataset was part of a larger Y2H screen (GEO GSE150396) to identify novel proteins involved in barley immune responses. Yeast-two-hybrid (Y2H) screening was coupled with next-generation sequencing to identify and quantify interacting proteins. An AVRA1 bait was mated to a cDNA prey library derived from a 0-48 hour time course of infected leaf tissue. Screens were performed in batch liquid culture to enrich yeast populations for cells expressing positive interactions. After two rounds of enrichment under selective (Histidine absent) and non-selective (Histidine present) conditions, yeast cells were collected. Y2H plasmids were extracted and prey cDNA amplicons were generated via low-cycle PCR. Fragmented amplicons were used as input to generate sequencing libraries and processed on the HiSeq 3000 platform. Reads were mapped to the barley and Blumeria graminis genomes and read counts were analyzed using a custom data processing and scoring pipeline. Putative interactors were cloned and binary Y2H was used to confirm interactions.