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SRX898071: RiboSeq of human: fibroblasts: Sample S2.Riboseq2.15
1 ILLUMINA (Illumina HiSeq 2000) run: 46.7M spots, 1.9G bases, 1.1Gb downloads

Design: Ribosomal profiling was performed using cycloheximide, following Ingolia et al. 2012 (Nature Protocols). The basic profiling protocol comprises cell or tissue lysis, nuclease footprinting, ribosome purification, and sequencing library generation and validation. Cells or tissues are rapidly lysed with detergent and the lysates are digested with E. coli RNase I in order to degrade mRNA not protected by the ribosome. Ribosomes, containing protected mRNA footprints, are purified by sedimentation through a sucrose cushion during ultracentrifugation. mRNA is recovered by gel size-selection from the ribosomal pellet and used to generate a sequencing library using an approach optimized for low sequence bias. For which we usually use small RNA Tru-seq kit from Illumina.
Submitted by: NICHD-phs000645
Study: Loss of cytosine-5 methylation in tRNA triggers stress responses in a disease model for Intellectual Disabilities
show Abstracthide Abstract
Mutations in the cytosine-5 RNA methyltransferase NSun2 can cause neurodevelopmental disorders and symptoms commonly found in patients with Dubowitz-like syndrome. Some tRNAs are known to be methylated NSun2, however the occurrence of cytosine-5 methylation (m<sup>5</sup>C) in other RNA biotypes is still under debate. Location in RNA and function of m<sup>5</sup>C has not been studied yet. This study is aimed at identifying new m<sup>5</sup>C methylated RNA biotypes, as well as the location at specific structures or sequences and the ultimate biological function. The impact of the loss of NSun2-mediated methylation is also determined by comparing gene expression data with the global cytosine-5 RNA methylome in Dubowitz-like syndrome patients. We also use ribosomal profiling to assess the impact of the loss and rescue of Nsun2-mediated cytosine-5 RNA methylation on translation rates and ribosome occupancy.
Sample: RNA fragments from ribosomal profiling sample from Skin/Dermal fibroblast of a human participant in the dbGaP study "Location and Function of Cytosine-5 Methylation in RNA"
SAMN03320075 • SRS863212 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: S2.Riboseq2.15
Instrument: Illumina HiSeq 2000
Strategy: OTHER
Source: TRANSCRIPTOMIC
Selection: other
Layout: SINGLE
Spot descriptor:
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The SRA run(s) below contain human sequence (more...)(less...)

These data are available through the dbGaP authorized access system. Request access to:

  • Study:  phs000645
  • Consent Group: GRU

Runs: 1 run, 46.7M spots, 1.9G bases, 1.1Gb
Run# of Spots# of BasesSizePublished
SRR182784846,656,0301.9G1.1Gb2015-05-27

ID:
1292105

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