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| Status |
Public on Mar 02, 2015 |
| Title |
ribo_wild-type DED1 replicate 1_15 deg |
| Sample type |
SRA |
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| Source name |
Whole cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain (genetic background): wild-type DED1 (NSY4)
temperature: 15 deg
molecule type: Ribosome-protected RNA
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| Treatment protocol |
All cultures were treated with cycloheximide (100 ug / ml) for 2 min prior to harvesting
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| Growth protocol |
Cells were generally grown to an OD600 of ~ 0.7 in synthetic complete medium and subjected to temperature shifts as indicated
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were rapidly vacuum filtered and flash frozen. Whole cell extracts were prepared by breaking cells in freezer mill.
Ribosome profiling (Rnase I footprinting, size selection,RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324(5924):218-223
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Experiment 1
processed data file: ded1-cs.csv
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| Data processing |
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with bowtie2 v2.0.6
Transcriptome alignment with TopHat v2.0.7
Read quantitation using custom scripts
Analysis of reads using DESeq
Genome_build: sacCer2
Supplementary_files_format_and_content: processed txt (csv) files per experiment show a matrix (with columns: yORF name, gene name, WT ribosome occupancy, mutant ribosome occupancy, WT mRNA occupancy, mutant mRNA occupancy, ribosome occupancy change, mRNA occupancy change, TE change). All numerical columns have log values with base 2
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| Submission date |
Mar 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Alan G Hinnebusch |
| E-mail(s) |
[email protected]
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| Organization name |
NICHD
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| Street address |
6 CENTER DR Room 230, MSC 0609
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platform ID |
GPL13821 |
| Series (1) |
| GSE66411 |
Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A |
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| Relations |
| BioSample |
SAMN03381341 |
| SRA |
SRX894007 |
| 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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