Bisulfite-seq in Arabidopsis thaliana Col and hcr2 mutant
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ABSTRACT: DNA-prep of Col and hcr2 mutant from seedling and bud sample. DNA was extracted using DNeasy Plant Mini Kit (Qiagen 69104, USA). Library construction and bisulfite conversion was performed using EZ DNA Methylation-Gold kit (ZYMO). DNA libraries are sequenced on the DNBseq platform (BGI, Hong Cong).
Project description:RNA-prep of Col and hcr3 mutant from seedling or bud sample. RNA was extracted using the RNeasy plant (Qiagen, 74904) and sent to BGI Hongkong for RNA-seq library construction and sequencing. Briefly, mRNA enriched by using oligo dT beads were fragmented and used for cDNA synthesis. dUTP method was used for cDNA synthesis to make the RNA-seq library strand-specific. The constructed library was amplified to make DNA nanoball (DNB) and sequenced on DNBSEQ platform.
Project description:RNA-prep of j3-1, j3-3, j2-2, hcr3 mutant from seedling or bud sample. RNA was extracted using the RNeasy plant (Qiagen, 74904) and sent to BGI Hongkong for RNA-seq library construction and sequencing. Briefly, mRNA enriched by using oligo dT beads were fragmented and used for cDNA synthesis. dUTP method was used for cDNA synthesis to make the RNA-seq library strand-specific. The constructed library was amplified to make DNA nanoball (DNB) and sequenced on DNBSEQ platform.
Project description:ATAC-seq of Col and hcr2 mutant from seedling and bud sample. Tagmentation was performed using the Tag DNA enzyme & buffer kit (Illumina, 20034210). Nextera DNA CD Index primers were used for library construction. The indexed libraries were subjected to paired-end 50-bp sequencing using an Illumina HiSeqX instrument (Microgen, Korea).
Project description:To identified the differential methylation of genes and regions to elucidate the mechanisms of toxicity related to environmental chromium exposure. Fasting whole blood samples were collected by clinicians in ethylenediaminetetraacetic acid (EDTA) anticoagulant tubes, and stored them at −80 °C. A DNeasy Blood and Tissue Kit (Qiagen) was used to isolate DNA from whole blood. The purity and concentration of DNA were estimated using Nanodrop 2000 (ThermoScietific). Approximately 500 ng of genomic DNA from each sample was used for sodium bisulfite conversion with the EZ DNA methylation Gold Kit (Zymo Research, USA) in accordance with the manufacturer’s standard protocol. Genome-wide DNA methylation was performed using the Illumina Infinium HumanMethylation850K (EPIC) BeadChip (Illumina Inc, USA) in accordance with the manufacturer’s instructions.
Project description:Col and hcr2 mutant from seedling and bud sample were harvested. Nuclei extracted using Honda buffer. Cross-linked chromatin was fragmented with mirococcal nuclease (MNase, NEB M0247S). After fragmentation, fragmented chromatin was incubated with H3K4me3 antibody (AbCam ab8580). TruSeq Prep Kit v2 (Illumina) were used for library construction.
Project description:RNA-prep of Col and hcr2 mutant from seedling and bud sample. RNA extracted by Trizol and cDNA was synthesized by using the ScriptSeq v2 RNA-seq Library Preparation Kit (SSV21124, Epicentre). ScriptSeq Index PCR Primers (RSBC10948, Epicentre) were used for library construction.
Project description:Genomic DNA from 55 wild type Col x Ler F2 individuals was extracted using the CTAB method. Equal amounts of DNA from these 55 plants were pooled into two groups (pool 1 = 4 plants; pool 2 = 51 plants), and nine micrograms of gDNA from each pool was used to generate Nanopore sequencing libraries with the Ligation Sequencing Kit V14 (Nanopore, SQK-LSK114). The libraries were sequenced independently using PromethION (BGI, Hong Kong).
Project description:To establish contamination profiles, the sperm donors with normal sperm counts were analyzed using an Infinium HumanMethylation450 array. Somatic cell lysis, sperm isolation, DNA extraction, and bisulfite conversion were performed as described by Aston et al. The bisulfite converted sperm DNA was hybridized to Illumina Infinium HumanMethylation450K microarrays at the University of Utah and run as recommended by the manufacturer (Bibikova et al. 2011). Unpaired blood samples were extracted using Qiagen's DNeasy Blood and Tissue kit and bisulfite converted using Zymo's EZ DNA Methylation kit. All procedures were performed according to the instructions of the manufacturer. Four permutations were run on each sample, including pure blood, half blood and half sperm by DNA concentration, half blood and half sperm by cell count, and pure sperm (n = 16). Concentration was normalized using a spectrophotometer. A Makler cell counting chamber was used to count white blood cells and sperm, which were then normalized in a 1:1 ratio.
Project description:The experiment looks for diurnal-regulated genes in Medicago truncatula plants. Medicago truncatula Jester accession plants were entrained for18 days in long days (16h light:8h dark) at 24°C constant temperature. Samples for two biological replicates per time point were collected every 4h for 24h beginning at ZT0 (subjective dawn) until ZT20. Total RNA was extracted from ground tissue using an RNeasy RNA extraction kit (Qiagen). Extracted total RNA was DNAse-treated (Invitrogen). Total RNA (2-3ug) was dried down and preserved in Sigma-Aldrich RNAstable before being couriered to BGI Tech Solutions (HONGKONG) Co., Ltd (https://www.bgi.com/global). BGI Tech prepared and processed libraries for 20M PE100 reads using their DNBseq platform - BGISEQ-500.
Project description:We have worked on skin explants and activated T cells locally with a CD3 antibody, whole biopsies were activated, then epidermal and dermal RNA was sequenced. Sequencing was performed by BGI (Hong Kong) as well as the group analysis.