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Sample GSM1557443 Query DataSets for GSM1557443
Status Public on Jan 05, 2015
Title ACA-K mrna
Sample type SRA
Source name yeast
Organism Saccharomyces cerevisiae
Characteristics strain: S288C
Treatment protocol Cells were filtered and frozen on liquid nitrogen
Growth protocol Yeast were grown to OD=0.6
Extracted molecule total RNA
Extraction protocol Total RNA was isolated with hot acid phenol. mRNA was selected using oligo dT Dynabeads
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer II
Description 3/4 copies of Threonine tRNA (tT(UGU)G2, tT(UGU)H, tT(UGU)P), recognizing the ACA codon, were knocked out using the standard technique of homologous recombination from a plasmid PCR product. The resulting strain was marked with nourseothricin, kanamycin, and hygromycin B resistance respectively. Successfully transformed yeast were identified by check PCR.
Data processing Raw fastq files were stripped of the linker sequence (CTGTAGGCACCATCAAT) using the FASTX-Toolkit v0.0.13 clipper.
Reads were aligned to the yeast genome (R63 from SGD, using bowtie v1.0.0 and the following parameters (-l 18 -n 2 -v 2 -m 1 -k 1). Namely, only uniquely mapped reads with less than two mismatches were kept.
The final processed mRNA and fooprint counts are filtered for the mRNA reads with length greater than 26 and footprint reads with length between 28 and 31 inclusive.
Genome_build: R63
Supplementary_files_format_and_content: Processed txt files per sample show a matrix (with columns: gene name, gene length, total mRNA counts, total ribosome footprint counts, and the ribosome footprint counts per position) for the reliable genes in each sample.
Submission date Dec 02, 2014
Last update date May 15, 2019
Contact name Cristina Pop
Organization name Stanford University
Department Computer Science
Street address 353 Serra Mall
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platform ID GPL9377
Series (1)
GSE63789 Causal signals between codon bias, mRNA structure and the efficiency of translation and elongation
BioSample SAMN03248317
SRA SRX793379

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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