s1421s  (New England Biolabs)

Journal: bioRxiv

Article Title: Chromatin run-on reveals the transcriptional etiology of glioblastoma multiforme

doi: 10.1101/185991

Figure Lengend Snippet: ChRO-seq and leChRO-seq measure primary transcription in isolated chromatin. (a) Isolated chromatin is incubated with biotinylated rNTPs, purified by streptavidin beads, and sequenced from the 3’ end. leChRO-seq degrades existing RNA, extends nascent transcripts an average of 100 bp, and sequences RNAs from the 5’ end. (b and c) Comparison between matched ChRO-seq and PRO-seq in annotated gene bodies (b) or at the peak of paused Pol II (c) in units of reads per kilobase per million mapped. (d) Comparison between ChRO-seq (top three tracks), PRO-seq (center), and H3K27ac ChlP-seq, DNase-I-seq, and RNA-seq (bottom). dREG-HD shows the raw signal fordREG (gray) and imputed DNase-I hypersensitivity signal (dark red). (e) The distribution of read lengths from ChRO-seq (blue) and leChRO-seq (pink) in a 30 year old primary GBM.

Article Snippet: Nascent RNA was purified by binding streptavidin beads (NEB # S1421S) and washed as described .

Techniques: Isolation, Incubation, Purification, RNA Sequencing Assay

Journal: Nature Communications

Article Title: SMRT-Cappable-seq reveals complex operon variants in bacteria

doi: 10.1038/s41467-018-05997-6

Figure Lengend Snippet: SMRT-Cappable-seq identifies full-length transcripts in bacteria. a Schema of the SMRT-Cappable-seq methodology. 5′ triphosphorylated transcripts are capped with a desthio-biotinylated (DTB) cap analog and bound to the streptavidin beads to specifically capture primary transcripts starting at TSS. The polyadenylation step (A-tailing) ensures the priming of the anchored poly dT primer for cDNA synthesis at the most 3′end of the transcript. b Integrative Genomics Viewer (IGV) representation of the mapping of SMRT-Cappable-seq reads (top) compared to Illumina RNA-seq reads (bottom) in the mprA locus. Forward oriented reads are labeled in pink, reverse oriented reads are labeled in blue. c Comparison between gene expression level in Read counts Per Kilobase of transcript, per Million mapped reads (RPKM) for Illumina RNA-seq and SMRT-Cappable-seq. The Spearman’s rank correlation is 0.798 ( p value

Article Snippet: The capped RNA was enriched using hydrophilic streptavidin magnetic beads (New England Biolabs).

Techniques: RNA Sequencing Assay, Labeling, Expressing

Journal: PLoS ONE

Article Title: Efficient multi-gene expression in cell-free droplet microreactors

doi: 10.1371/journal.pone.0260420

Figure Lengend Snippet: DNA immobilization on beads and expression in ¼l-scale reactions. (a) Comparison of fluorescent protein expressed in 25 μ l reactions from DNA in solution or equivalent amounts of DNA directly immobilized on beads. Error bars show standard deviation calculated from three replicates. (b) Optimization of direct DNA loading: biotinylated dsDNA fragments of various sizes were incubated with Streptavidin-coated micro beads. Dashed lines: DNA binding efficiency.

Article Snippet: For Golden Gate assembly or Bxb1 recombination, the first linear DNA fragment with either a BsaI restriction site or a Bxb1 recombination site at the 3’ terminal (following the T7 terminator), was bound to streptavidin beads as described above.

Techniques: Expressing, Standard Deviation, Incubation, Binding Assay