In ChAR-seq, proximity ligation of RNA and DNA to a linker molecule is used to construct a chimeric RNA-DNA molecule that is converted to DNA for sequencing. In a single assay, ChAR-seq can discover de novo chromatin interactions of distinct RNAs, including nascent transcripts, splicing RNAs...
Single-cell RNA-seq Single-cell RNA sequencing (scRNA-seq) libraries were prepared using 6000 mES cells, either in a wild type state or treatment with 1,6-hexanediol at 1.5% or 2,5-hexanediol at 1.5% for 30 min, and K562 cells (National Collection of Authenticated Cell Cultures, TCHu...
RNA Sequencing and analysis Total RNA from cells transfected with siRNA for the time indicated were prepared with RNeasy Mini kit (QIAGEN) and treated with ribo-Zero kit (illumina) to remove ribosomal RNA. RNA-seq libraries were prepared with a NEBNext® Ultra RNA Library Prep Kit for Illum...
a lncRNA transcribed from telomeres, has been identified as a telomere-associated regulator of chromosome end protection [128]. Thus, intracellularly, TERRA plays a crucial role in telomere length homeostasis. A recent study reported that TERRA ...
RNA-seq library preparation and RNA isoform analysis Total RNA from LCLs was isolated using Trizol (Ambion) and the RNeasy Mini Kit (Qiagen). RNA-seq libraries and 75-bp or 100-bp paired-end sequencing were undertaken at the Genomic Units from Centre Nacional d’Anàlisi Genòmica (CNAG) ...
MNase has been used in various types of chromatin studies. It was most commonly used to study nucleosome occupancy and positioning in eukaryotic genomes, which can be accomplished by sequencing mononucleosomal DNA fragments generated from MNase digestion [26]. Sequencing of DNAs derived from different...
After PCR, the DNA product between 300-750bp was purified by gel extraction using DNA recovery kit (Zymo, #D4002) for deep sequencing. (Optional) Step 6. SMART-seq based RNA-seq libraries constructed using RNAs collected from HiCAR procedure. The cytoplasmic and nuclei RNA fraction was ...
We present a gene-level regulatory model, single-cell ATAC + RNA linking (SCARlink), which predicts single-cell gene expression and links enhancers to target genes using multi-ome (scRNA-seq and scATAC–seq co-assay) sequencing data. The approach uses regularized Poisson regression on tile...
Recently, the availability of DRIPc-seq (DNA:RNA hybrid immunoprecipitation followed by sequencing of the cDNA derived from the RNA moiety of hybrids) and OK-seq data (Okazaki fragment sequencing)25 in K562 cells allowed us to predict genomic sites prone to TRCs26. Here, we show that in ...
RNA sequencing Approximately 1 × 104 MCF-7 or ADR cells were collected and washed three times with ice-cold PBS. RNA extraction was performed using TRIzol reagent (Invitrogen). rRNA and genomic DNA were removed using a MICROBExpress Kit (Ambion) and DNase I (Invitrogen). The RNA was ...