ATAC-seq in Arabidopsis thaliana Col and hcr2 mutant
Ontology highlight
ABSTRACT: 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: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: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:We sequenced messenger RNA isolated from seeding, root, and floral bud tissue for 2 MAGIC founder accessions of Arabidopsis thaliana. The resulting data was used for validation of gene models, and provides a resource to assess tissue-specific expression. Examination of RNA expression across tissues (seedling, root, floral bud) for 2 accessions (Col-0, Can-0).
Project description:We produced RNA-Seq reads from messenger RNA isolated from seedling, root, and floral bud tissue for 17 MAGIC founder accessions (inbred strains) of Arabidopsis thaliana (see Gan et al. 2011. Nature, 477:419-23 for a description of the MAGIC genetic mapping resource). The resulting RNA-Seq data provide a resource to assess tissue-specific expression across different accessions of A. thaliana. Note that comparable read data for accessions Col-0 and Can-0, which are also founders of the MAGIC lines, has previously been released under GEO series GSE30795 (Gan et al. 2011. Nature, 477:419-23). Examination of RNA expression across tissues (seedling, root, floral bud) for 17 Arabidopsis thaliana accessions (Bur-0, Ct-1, Edi-0, Hi-0, Kn-0, Ler-0, Mt-0, No-0, Oy-0, Po-0, Rsch-4, Sf-2, Tsu-0, Wil-2, Ws-0, Wu-0, Zu-0).
Project description:For protein identification, the following parameters were used. Peptide mass tolerance = 20 ppm, Missed cleavage = 2, MS/MS tolerance = 0.1 Da, Enzyme = Trypsin, Fixed modification: Carbamidomethyl (C), iTRAQ8plex(K), iTRAQ8plex(N-term), Variable modification:Oxidation(M),Decoy database pattern=Reverse. The MASCOT search results for each SCX elution were further processed using the ProteomicsTools (version 3.1.6) which includes the programs BuildSummary, Isobaric Labeling Multiple File Distiller and Identified Protein iTRAQ Statistic Builder (Information can be accessed from Research Center for Proteome Analysis (http://www.proteomics.ac.cn/).
Project description:A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were isolated, lysed and barcoded in droplets. Droplets were then disrupted and cDNA was pooled for second strand synthesis. Libraries were generated with direct tagmentation followed by 3’ enrichment and sample indexing using Illumina Nextera library prep kit. Pooled libraries were sequenced on the Illumina NextSeq500 sequencer. Sequencing data were primarily analyzed using the SureCell RNA Single-Cell App in Illumina BaseSpace Sequence Hub.