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Sample GSM3141477 Query DataSets for GSM3141477
Status Public on Jan 18, 2019
Title exp.2_wt-Hel2-HTP
Sample type SRA
 
Source name wt-Hel2-HTP
Organism Saccharomyces cerevisiae
Characteristics 5'-linker identifier: NNNACTCAGC
additional notes: 2 size fractions
molecule: protein-crosslinked RNA
Treatment protocol Cells were crosslinked for 100s and harvested by centrifugation.
Growth protocol Cells were grown in SD media lacking Trp and containing 2% glucose to OD600 0.5.
Extracted molecule total RNA
Extraction protocol Cells were lysed, UV-crosslinked protein-RNA complexes were purified by tandem purification on IgG, TEV cleavage and immobilisation on Ni-NTA.
Libraries were constructed using the published CRAC protocol with minor modifications (Granneman et al., 2009).
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model Illumina MiniSeq
 
Description CRAC sample
Data processing Library strategy: CRAC
Base calling was done using Illumina standard software.
Data were split according to i7 indices using Illumina software.
Reads from different lanes belonging to the same sample were concatenated.
Reads were split according to in-line barcodes.
For submission to GEO, reads from the same sample, but carrying different i7 indices, and for exp.1 and exp.2 from two different size fractions, were combined and only identical parts of a5'-linkers were removed, while random nucleotides and parts of the 5'linkers that differed between samples were retained. For further data processing, these parts were removed.
Further processing: 3'-adapters were removed using flexbar. pyFastqDuplicateRemover.py from the pyCRAC package (Webb et al., 2014) was used to collapse data (files belonging to the same sample but with different indices & 5'linkers with 3'-terminal N were treated separately, as reads definitely result from separate RNA molecules, to retain greater sequencing depth and collapsed files were combined thereafter - available upon request).
Collapsed and uncollapsed data were aligned using novoalign. Reads were mapped using pyReadCounters from the pyCRAC package. Bedgraphs were generated from pyReadCounters output and converted to bigwig format using bedGraphToBigWig.
Genome_build: sacCer3, EF4.74
Supplementary_files_format_and_content: bedgraph files showing hit density (actual counts) for aligned, collapsed data.
 
Submission date May 14, 2018
Last update date Jan 18, 2019
Contact name Marie-Luise Winz
E-mail(s) marie.luise.winz@gmail.com
Organization name University of Edinburgh
Department Wellcome Centre for Cell Biology
Lab Tollervey Lab
Street address Max Born Crescent
City Edinburgh
ZIP/Postal code EH9 3BF
Country United Kingdom
 
Platform ID GPL22715
Series (2)
GSE114420 Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control [II]
GSE114429 Molecular interactions between Hel2 and RNA supporting ribosome-associated quality control
Relations
BioSample SAMN09206833
SRA SRX4081737

Supplementary file Size Download File type/resource
GSM3141477_exp.2_wt-Hel2-HTP_count_output_reads.gtf_minus_strand_reads.bedgraph.gz 305.5 Kb (ftp)(http) BEDGRAPH
GSM3141477_exp.2_wt-Hel2-HTP_count_output_reads.gtf_plus_strand_reads.bedgraph.gz 261.5 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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