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...
9b,c). Furthermore, to examine transcriptome changes in DAXX-kd/PTEN-null GBM cells we performed RNA sequencing (RNA-seq) (Supplementary Fig. 11a). Of the 1,403 genes showing differential expression (DiffExp) between cells treated with shControl and cells treated with shDAXX, there were ...
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...
Processing of PAR-CLIP RNA samples for sequencing. (a) Outline of experiments. PAR-CLIP of endogenous PARP1 was performed on HeLa cells using 4-thiouridine (4SU). (b) PAR-CLIP samples run on an SDS PAGE gel were imaged with Typhoon. (c) Protein-bound samples were transferred onto a ni...
3D disorganization and rearrangement of genome provide insights into pathogenesis of NAFLD by integrated Hi-C, Nanopore, and RNA sequencing chromatin interaction map was generated to examine different 3D genome hierarchies including A/B compartments,topologically associated domains(TADs),and chromatin... ...
To better understand how Trim24 functions mechanistically in mouse ESCs, we performed knockdown of Trim24 using short hairpin RNA (shRNA) for 24 hr, followed by mRNA sequencing. We observed dysregulation of 1,562 genes (adjusted p value < 0.01 and fold change >1.5) (Figure 4D; Table S4A)...
We used the bamCoverage function in deepTools (v3.5.0) (Ramírez et al., 2016) to normalize the whole-gene ATAC-seq signals in 50 bp windows with bins per million mapped reads (BPM), similar to TPM in RNA-sequencing. The bw files were obtained using the computeMatrix function to ...
63-WT transfection without ABA treatment (Fig.6b), which supported the sequencing result that formation of the spatial cluster was a stress signal-dependent process (Fig. S11a). In all, this case study elucidates the essentiality of OsbZIP23-mediated DS-specific PPI clusters to the co-...
Total RNA was isolated from control non-targeting siRNA and PARP1 knockdown (KD) cells, and poly(A)-selected mRNA sequencing was performed on the Illumina platform. Biological replicas from RNA-seq showed high Pear- son correlation (Supplementary Table S4), allowing pooling of samples for ...