Global landscape of replicative DNA polymerase usage in the human genome
E Koyanagi, Y Kakimoto, T Minamisawa… - Nature …, 2022 - nature.com
… termination close to transcription start sites and show that transcription can perturb the …
libraries for Illumina sequencing. Approximately 200 million paired-end reads were obtained per …
libraries for Illumina sequencing. Approximately 200 million paired-end reads were obtained per …
Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells
I Zanin, E Ruggiero, G Nicoletto, S Lago… - Nucleic Acids …, 2023 - academic.oup.com
… at gene promoters, close to the transcription start site (TSS), but … Samples were sequenced
paired-end on an Illumina … Here, we investigated and compared the iM- and G4-landscape …
paired-end on an Illumina … Here, we investigated and compared the iM- and G4-landscape …
Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue
… region-specific epigenetic landscapes in mouse embryos … are usually found proximal to the
transcription start site (TSS) … are sequenced using paired-end sequencing corresponding to …
transcription start site (TSS) … are sequenced using paired-end sequencing corresponding to …
Combining TSS-MPRA and sensitive TSS profile dissimilarity scoring to study the sequence determinants of transcription initiation
C Guzman, S Duttke, Y Zhu… - Nucleic Acids …, 2023 - academic.oup.com
… the transcription initiation landscape of endogenous sequences, we developed a windowed
… by paired-end sequencing and aligning the cloned sequences to the original sequences …
… by paired-end sequencing and aligning the cloned sequences to the original sequences …
Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis
… To explore the resulting chromatin landscape, we defined open … resulting peak list with
known transcription start sites (TSS) to … were sequenced with NextSeq500 (three 50 paired-end …
known transcription start sites (TSS) to … were sequenced with NextSeq500 (three 50 paired-end …
From reads to insight: a hitchhiker's guide to ATAC-seq data analysis
… to decipher the epigenetic landscape. These include Assay … Paired-end sequencing is then
performed to facilitate higher … to be enriched around the transcription start site (TSS) of genes, …
performed to facilitate higher … to be enriched around the transcription start site (TSS) of genes, …
RNA structure landscape of S. cerevisiae introns
… find the most prominent transcription start site upstream of the … sequences and ensuring
consistency between paired-end … We then merged paired-end reads using bbmerge 101 with …
consistency between paired-end … We then merged paired-end reads using bbmerge 101 with …
Identification of plant transcription factor DNA-binding sites using seq-DAP-seq
… are PCR-amplified, barcoded if necessary, and sequenced using paired-end sequencing …
TF, with sequencing data from an ampDAP-seq experiment with paired end reads with two …
TF, with sequencing data from an ampDAP-seq experiment with paired end reads with two …
Chromatin accessibility profiling methods
L Minnoye, GK Marinov, T Krausgruber, L Pan… - Nature Reviews …, 2021 - nature.com
… a chromatin landscape is shown in which transcription … sequencing (ChIP–seq) and related
methods, as these are powerful techniques to gain further insights into chromatin landscapes …
methods, as these are powerful techniques to gain further insights into chromatin landscapes …
Precise transcript reconstruction with end-guided assembly
… transcript start and end sites is essential for precise transcript … aimed to reconstruct transcripts
from paired-end short reads. … sequenced, with an average of 7 million aligned paired-end …
from paired-end short reads. … sequenced, with an average of 7 million aligned paired-end …