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Sample GSM6808147 Query DataSets for GSM6808147
Status Public on May 01, 2024
Title DES7S_RiboSeq_rep1
Sample type SRA
 
Source name Yeast strain yJD1046
Organism Saccharomyces cerevisiae
Characteristics condition: plasmid born deltaES7S rRNA sequence
molecule subtype: Ribosome protected fragments isolated via densitiy gradients
Growth protocol Yeast cells were grown in YPD media to OD = 0.8. Cells were harvested bySnap freezing, ground in a cryomill and lysates were cleared by centrifugation.
Extracted molecule total RNA
Extraction protocol Lysates were digested with RNAse1 and 80S ribosomes extracted from a density gradient after Ultracentrifugation. Size excluded RNA fragments were ligated to DeepSeq adapters.
mRNA fragments ranging rom 24-28nt were size excluded and dephosphorylated. Adapters were ligated and the resulting fragments were circularized. cDNA was prepared with circRNA as input and PCR amplicification was performed for 4-8 cycles.
 
Library strategy OTHER
Library source transcriptomic
Library selection other
Instrument model NextSeq 550
 
Data processing Reads were trimmed using the FastX-toolkit. 6 randomized Linkernucleotides at the 3'End and three at the 5'end were trimmed.
Quality of reads was assessed using FastQC (v0.11.7)
Processed reads were mapped against noncoding RNAs and afterward against annotated open reading frames elongated at both ends by 21nt using bowtie (v1.2.3) with settings "-v 1 -m 1 --norc --best --strata
Supplementary files format and content: counts
Library strategy: Ribo-seq
 
Submission date Dec 09, 2022
Last update date May 01, 2024
Contact name Robert Rauscher
E-mail(s) ag.polacek@gmail.com
Organization name University of Bern
Street address Freiestrasse 3
City Bern
State/province Bern
ZIP/Postal code 3012
Country Switzerland
 
Platform ID GPL26302
Series (1)
GSE220642 RiboSeq and mSeq of two yeast strains
Relations
BioSample SAMN32132223
SRA SRX18629703

Supplementary file Size Download File type/resource
GSM6808147_dES71_RPF_counts.txt.gz 28.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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