Project description:In this project, leaves and EBCs of the halophyte plant Chenopodium quinoa were treated with ABA. The effect of the ABA treatment was analyzed by comparing to non-treated leaves and EBCs.
Project description:Heterotrimeric G proteins mediate crucial and diverse signaling pathways in eukaryotes. To gain insights into the regulatory modes of the G protein and the co-regulatory modes of the G protein and the stress hormone abscisic acid (ABA), we generated and analyzed gene expression in G protein subunit single and double mutants of the model plant Arabidopsis thaliana. Through a Boolean modeling approach, our analysis reveals novel modes of heterotrimeric G protein action. Keywords: transcriptome analysis; G protein subunit mutants; abscisic acid (ABA) Microarray data were generated from four genotypes (wild type, gpa1-4 mutant, agb1-2 mutant, agb1-2 gpa1-4 double mutant) with or without ABA treatment. Arabidopsis plants were grown in growth chambers with an 8 hr light/16hr dark. Three hundred Arabidopsis leaves excised from 60-70 five-week-old plants were used as the starting material for each guard cell microarray. Ten mature leaves taken from 3-4 plants grown side-by side with the plants for guard cell isolation were used for each leaf sample. Excised leaf and isolated guard cell samples were treated with ABA (50 μM) or EtOH (solvent control) for 3 hrs. For each type of sample (guard cells or leaves), three independent biological replicates were performed, resulting in a total of 48 microarray hybridizations (2 sample types ´ 4 genotypes ´ two treatments ´3 replicates).
Project description:Genomic DNA of a Holstein male, that was used for multiple tissue ATAC-seq experiments, was sequenced. The sequences were used for ATAC-seq peak calling as a background.
Project description:4 weeks old rooted plantlets of P. × canescens (Clone INRA717 1-B4) were cultivated in hydroponics in 2 l pots in Long Ashton nutrient solution in a culture room for 8 weeks before treatments started. Three treatments were applied to the plants: control treatment (-ABA), continuous 100 µM ABA treatment (+ABA) and discontinuous 100 µM ABA treatment (±ABA). ABA was fed to +ABA plants during the whole treatment period of 30 days. ABA was fed to ±ABA plants for three days in two weeks. Developing xylem and mature xylem were collected separately during the harvest and shortly frozen in liquid nitrogen. RNA was extracted from these samples and followed by RNA-sequencing.
Project description:RNA-seq upon TBX2 knockdown in the neuroblastoma cell line CLB-GA. Cells were transduced with two different shRNAs (sh#2 and sh#4) targeting TBX2 and a non-targeting control (NTC), and selected with puromycin. Analysis was performed seven days upon TBX2 knockdown, including three biological replicates per condition.
Project description:RNA-seq upon TBX2, MYCN or combination of TBX2 and MYCN knockdown in the neuroblastoma cell line IMR-5/75. Cells were transduced with two different shRNAs (shTBX2_2 and shTBX2_4) targeting TBX2 and a non-targeting control (NTC), and selected with puromycin. Cells were treated with doxycycline for shMYCN induction (with DOX or not). Analysis was performed three days upon TBX2 knockdown and two days upon MYCN knockdown, including six biological replicates per condition.
Project description:A knockout cell library in Huh7.5.1 cells was generated by introducing a genome-scale CRISPR library (GeCKOv2, Addgene #1000000049) and subjected to hepatitis A virus infection (HM175/18f) to isolate virus-resistant mutant cells. Genomic DNA was isolated from the original and virus-selected mutant cell populations and abundance of guideRNA encoding sequences were measured by sequencing on an Illumina NextSeq (High Output).
Project description:We measured genome-wide gene expression of embryonic stem cells derived from two different inbred mouse genetic backgrounds. For each genetic background we also conducted an allele swap at SNP rs50454566 upstream of the Lifr gene. We profiled cells from each of the four strains in triplicate (technical replicates). We cultured cells in media with LIF + GSK3-beta inhibitor CHIR99021. Cells remained unfed until harvest, six days later.