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| Status |
Public on Jan 05, 2015 |
| Title |
ACA-K mrna |
| Sample type |
SRA |
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| Source name |
yeast
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: S288C
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| Treatment protocol |
Cells were filtered and frozen on liquid nitrogen
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| Growth protocol |
Yeast were grown to OD=0.6
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with hot acid phenol. mRNA was selected using oligo dT Dynabeads
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
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| 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.
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| 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, www.yeastgenome.org) 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.
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| Submission date |
Dec 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Cristina Pop |
| Organization name |
Stanford University
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| Department |
Computer Science
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| Street address |
353 Serra Mall
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platform ID |
GPL9377 |
| Series (1) |
| GSE63789 |
Causal signals between codon bias, mRNA structure and the efficiency of translation and elongation |
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| Relations |
| BioSample |
SAMN03248317 |
| SRA |
SRX793379 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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