Dataset features

Specifications


Application: RNA-seq analysis, sRNA-seq analysis, ChIP-seq analysis
Number of samples: 17
Release date: Oct 15 2011
Last update date: Sep 13 2013
Access: Public
Dataset link Glucosylated hydroxymethyluracil (DNA base J) prevents transcriptional read-through in Leishmania

Experimental Protocol


We determined the exact location of base J in the genome of Leishmania by high-throughput sequencing of J containing DNA fragments. Samples were enriched for J-containing fragments by two independent methods: ChIP using an anti-J DNA antibody or by binding to a the J-binding protein JBP1. We studied the effect of loss of J on transcription using WT, JBP2 knockout (30-37% of WT level J), and JBP2 knockout cells grown in BrdU containing medium (13-16% of WT level of J). We used 6 RNA-seq libraries (three samples & two replica each) containing processed RNA products (transspliced and poly-adenylated) and 3 small RNA libraries representing the entire transcriptome.

Repositories


GEO

GSE32976

ArrayExpress

E-GEOD-32976

ENA

SRP008929

BioProject

PRJNA146423

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Contact


Gowthaman Ramasamy