KASP1-22
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00010001905 | EGA |
REPOSITORIES: EGA
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Project description:We have investigated the genomic response of Arabidopsis cell suspension culture under high light. Our main goal has been twofold: first, to establish whether chloroplasts in Arabidopsis cell suspension culture are functional and, as such, can act as sensors of adverse external stimuli leading to the activation of genomic defence responses in a manner similar to that described in whole plants exposed to a wide range of environmental stresses and; second, to distinguish which of the ROS that would be probably generated in the chloroplasts is predominant. Our functional genomic analysis has led us to conclude that singlet oxygen is the major ROS in Arabidopsis cell suspension culture under high light stress and that singlet oxygen production is responsible for a genomic activation associated with the biosynthesis and signalling pathway of several phytohormones that ultimately triggers accelerated cell death. After the ninth day of growth, a volume of 200 mL of Arabidopsis cell suspension culture with a cell density of approximately 150-200 mg/mL was placed in a glass vessel surrounded by a water bath to maintain constant temperature during the light treatment. Nine microarray experiments were designed and classified as follows: control 1âÂÂ3 (50 microE/m2/s), 1-h dark 1âÂÂ3 and high light 1âÂÂ3 (1800 microE/m2/s); where 1âÂÂ3 stands for the number of biological replicates. After each treatment, sample RNA was extracted and its quality evaluated. The transcriptomic analysis was performed using Affymetrix GeneChip Arabidopsis genome ATH1 arrays.
2010-07-29 | E-GEOD-22671 | biostudies-arrayexpress
Project description:The cfMethyl-Seq libraries of the serial plasma cfDNA samples from the four NSCLC patients were constructed following the standard protocol. 10 ng of cfDNA in the volume of 25 µl was used as input material. 5’-end dephosphorylation was done with 3 µl 10xCutSmart buffer and 2 µl quick CIP from NEB (Ipswich, MA) at 37 oC for 30 min then heat-inactivated at 80 oC for 5 min. The 3’-end blocking was done with 0.5 µl 10xCutSmart buffer, 3 µl 2.5 mM CoCl2, 1 µl terminal transferase (all from NEB), and 0.5 µl 1 mM ddGTP at 37 oC for 2 h followed by 75 oC for 20 min. The mixture was then purified with 2x AmpureXP beads (Beckman Coulter, Indianapolis, IN) and eluted in 21.5 µl RT-PCR grade water (Thermo-Fisher, Waltham, MA). Restriction digestion was done with 2.5 µl 10xCutSmart buffer and 1 µl MspI (NEB) for 18 h at 37  oC and 20 min at 65 oC . 0.5 µl 10xCutSmart buffer, 0.3 µl dACGTP mixture (100 mM dATP, 10 mM dCTP, 10 mM dGTP), 1 µl Klenow (exo-, 5U/µl, NEB) and 2.6 µl RT-PCR water, 0.6 µl 50 mM DTT (ThermoFisher) was added to the mixture for end repair and A-overhang addition with the program 30  oC for 20 min, 37 oC for 1 h and 75 oC for 20 min. Adapter ligation was then performed with 1 µl 10xThermoFisher HC T4 ligase buffer, 0.4 µl 100 mM ATP (ThermoFisher), 0.2 µl 50 mM DTT, 1 µl ThermoFisher HC T4 DNA ligase (30 Weiss Unit/µl), 5 ng home-made duplex UMI adapter with all the cytosines methylated (protocol adopted from Kennedy et al.) at 16 oC for 20 h and 65 oC for 20 min. Bisulfite conversion of the adapter-ligated product was carried out with QIAGEN EpiTect plus DNA bisulfite kit following their protocol for two rounds of conversion. The converted product was purified with Qiagen MinElute spin column and eluted with 20 µl RT-PCR water. PCR amplification was done using the NEBNext Multiplex Oligos for Illumina (2.5 µl of universal and index primer each) and 25 µl KAPA HiFi HotStart Uracil+ ReadyMix (Roche) with the following cycling conditions: 98  oC for 45 s, 15 cycles of 98  oC for 15 s, 60  oC for 30 s and 72  oC for 30 s, followed by a final extension at 72  oC for 5 min. The PCR product was purified with 1x AmpureXP beads and eluted with 30 µl EB buffer. DNA concentration was measured by Qubit 1xdsDNA HS assay. 5% TBE-UREA PAGE and bioanalyzer assay was performed as quality control on each library before sequencing.
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Project description:Bifidobacterium bifidum CAG:234 overview
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Project description:To obtain an overview of the methylome landscape in the developing pig skeletal muscle, 81 high-quality whole-genome bisulfite sequencing(WGBS) libraries that covered 27 developmental stages (3 biological replicates per stage) from embryonic day 33 (E33) to postnatal day 180 (D180) were produced by whole-genome bisulfite sequencing.
2020-09-01 | GSE157043 | GEO
Project description:This ArrayExpress experiment contains RNA-seq data from human tissues, generated by Michael Snyder's lab at Stanford University as part of the ENCODE project ( https://www.encodeproject.org/search/?type=Experiment ). Sample information was obtained from the ENCODE data coordination center and protocol information was obtained from the associated publication in PNAS (Lin et al., 2014, PubMed ID 25413365). All samples, except for the ovary, were sequenced with technical replicates. The second technical replicate was performed in May 2015 and was not part of the original Lin et al. 2014 publication. Technical replicates are marked in the âComment[technical replicate group]â column of sample-data-relationship format (SDRF) file for this record.
2016-01-21 | E-MTAB-4344 | biostudies-arrayexpress
Project description:Here, we conducted an tandem mass tag (TMT)-based proteomics analysis of apple fruit development over five growth stages. Our objective was to gain a global overview of the dynamics of apple fruit development and identify key regulatory networks and proteins that contribute to fruit development and the metabolism and accumulation of sugars and acids for fruit quality improvement.
2016-10-13 | PXD004568 | Pride
Project description:Application of Microdroplet PCR for Large-Scale Targeted Bisulfite Sequencing
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Project description:PCR analysis of ovine innate immune receptor gene fragments for polymorphism analysis
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Project description:Investigate changes in IL-23/Th17- and type I interferon-pathway biomarkers and gene responses, and measures of selectivity for TYK2 over Janus kinases (JAKs) 1–3, in patients with moderate to severe psoriasis receiving deucravacitinib.
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Project description:Anaylsis differentially expressed genes of mouse peri-implanted uteri comparing pre-implantation uteri (Day2, Day3 and Day4) with post-implantation uteri (Day6, Day7 and Day8) by microassay. This study has built a meaningful basis for future investigation in elucidating the molecular nature of maternal-fetal interactions during pregnancy establishment and maintenance. Pre-implantation uteri VS. Post-implantation uteri. Three biological replicates of each experiments: pre-implantation uteri (Day2, Day3 and Day4): 234, 234①, 234②; 3 mixture of post-implantation uteri (Day6, Day7 and Day8): 678, 678①, 678②. Two hybridizations were performed by using a reverse fluorescence strategy (Cy3, Cy5) for each sample.
2011-06-30 | E-GEOD-26615 | biostudies-arrayexpress