Project description:Kethoxal-assisted ssDNA sequencing (KAS-seq) is gaining popularity as a robust and effective approach to study the dynamics of transcriptionally engaged RNA polymerases through profiling of genome-wide single-stranded DNA (ssDNA). Its latest variant, spKAS-seq, a strand-specific version of KAS-seq, has been developed to map genome-wide R-loop structures by detecting imbalances of ssDNA on two strands. However, user-friendly, open-source, and specific bioinformatic analyzer for KAS-seq data are still lacking. Here we present KAS-Analyzer as a flexible and integrated toolkit to facilitate the analysis and interpretation of KAS-seq data. KAS-Analyzer can perform standard analyses such as quality control, read alignment, and differential RNA polymerase activity analysis. In addition, KAS-Analyzer introduces many novel features, including, but not limited to: calculation of transcriptional indexes, identification of single-stranded transcribing enhancers, and high-resolution mapping of R-loops. We use benchmark datasets to demonstrate that KAS-Analyzer provides a powerful framework to study transient transcriptional regulatory programs. KAS-Analyzer is available at https://github.com/Ruitulyu/KAS-Analyzer.

2022-07-27 | GSE202044 | GEO

Transcript abundance comparison between BALB/c ears inoculated with Leishmania mexicana and Leishmania mexicana plus promastigote secretory gel (PSG)

Project description:To determine the modulation of gene expression of Leishmania mexicana(M379)-inoculated BALB/c ears in the presence of promastigote secretory gel (PSG) A genome-wide transcriptional analysis was performed by comparing the gene expression profiles of Leishmania mexicana- inoculated BALB/c ears and Leishmania mexicana plus PSG BALB/c ears. Leishmania mexicana amastigotes were purified from mouse cutaneous lesions and transformed in vitro in metacycic promastigotes (MT). After 6, 24 and 48 hours, ears were collected and processed for RNA extraction. Three Biological replicates per condition were run.

2013-12-17 | E-GEOD-52101 | biostudies-arrayexpress

Geohintonia mexicana

Project description:Geohintonia mexicana genome sequencing

| PRJNA853315 | ENA

RNA-seq analysis of Arabidopsis sulki1, Kas-2 and Ler/Kas-2 near isogenic line (NIL)

Project description:Progeny from a cross of Arabidopsis thaliana Landsberg (Ler, Poland) and Kashmir-2 (Kas-2, central Asia) accessions exhibit immune-related hybrid incompatibility (HI) due to a genetic interaction between a cluster of eight TNL (Toll/Interleukin1 Receptor- Nucleotide Binding - Leucine Rich Repeat) RPP1-like (Recognition of Peronospora parasitica 1-like) genes (R1- R8) from Ler and central Asian alleles of a Strubbelig-family receptor-like kinase (SRF3). In characterizing mutants altered in Ler/Kas-2 HI, we mapped multiple intragenic mutations to the RPP1-like Ler locus. The expression of sulki1 (suppressor of Ler/Kas-2 incompatibility 1) mutant mapping to RPP1-like R8 Ler, the parental line Kas-2 accession and the Ler/Kas-2 NIL have been determined by RNA-seq in 5-week old plants grown at 14 - 16 ºC.

2018-05-16 | E-MTAB-6755 | biostudies-arrayexpress

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