Journal: Molecular cell

Article Title: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes

doi: 10.1016/j.molcel.2019.10.032

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: BBTools (v37.90) , BBTools , https://sourceforge.net/projects/bbmap/.

Techniques: Control, Virus, Recombinant, Multiplex Assay, HDAC Activity Assay, Methylation Sequencing, Gene Expression, Chromatin Immunoprecipitation, Software

Journal: Developmental biology

Article Title: DNA methylation dynamics underlie metamorphic gene regulation programs in Xenopus tadpole brain

doi: 10.1016/j.ydbio.2020.03.013

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: ​ Reagent or resource Source Identifier Antibodies Rabbit polyclonal antiserum to 5-hmC Diagenode C15410205-20 Rabbit polyclonal antiserum to 5-caC Diagenode C15410205-20 Rabbit polyclonal antiserum to xTET3 This paper N/A Bacterial and Virus Strains Biological Samples Chemicals, Peptides, and Recombinant Proteins Critical Commercial Assays MethylCap kit Diagenode, Denville, NJ C02020010 (AF-100-0048) TruSeq mRNA Sample Prep v2 kit Illumina Inc., San Diego, CA RS-122-2001 DNA modification kit Epigentek, Farmingdale, NY P-1026-050 Deposited Data Raw and analyzed MethylCap-seq data This paper GSE139267 Raw and analyzed RNA-seq data This paper GSE140120 Experimental Models: Cell Lines Experimental Models: Organisms/Strains Xenopus tropicalis , Nigerian strain Xenopus One (Dexter, MI) Xenopus laevis Xenopus One (Dexter, MI) Oligonucleotides Primers for RTqPCR – see Supplemental Table 4 This paper N/A Primers for synthesizing spike-in controls using lambda DNA as template – see Supplemental Table 4 This paper N/A Primers for monitoring spike-in controls after methylated DNA capture using RTqPCR – see Supplemental Table 4 This paper N/A Primers for methylation-sensitive restriction digest/qPCR assays – see Supplemental Table 4 This paper N/A Primers for MethylCap-qPCR assay – see Supplemental Table 4 This paper N/A Primers for bisulfite sequencing – see Supplemental Table 4 This paper N/A Primers for subcloning xtet3 cDNA – see Supplemental Table 4 This paper N/A Recombinant DNA Software and Algorithms BBTools suite (v37.90) BBMap – Bushnell B. https://sourceforge.net/proiects/bbmap/ Samtools v1.8 Li et al., 2009 https://sourceforge.net/proiects/samtools/ PePr (v1.1.18) Zhang et al., 2014 https://github.com/shawnzhangyx/PePr/ bowtie2/RSEM (v2.1.0) Langmead and Salzberg, 2012 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Methprimer software Li and Dahiya, 2002 https://www.urogene.org/methprimer/ Other Open in a separate window KEY RESOURCES TABLE Using Methylated DNA Capture-sequencing, we discovered changes in DNA methylation at discrete regions of the tadpole neural cell genome during metamorphosis, with the largest changes occurring during the period from metamorphic climax to the completion of metamorphosis when 80% of the changes represented demethylation.

Techniques: Recombinant, Sample Prep, Modification, Lambda DNA Preparation, Methylation, Methylation Sequencing, Subcloning, Software