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| Status |
Public on Mar 01, 2018 |
| Title |
mRNA_ded1-ts(hcDBP1)_ replicate 2_37 deg |
| Sample type |
SRA |
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| Source name |
Whole cells
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain (genetic background): ded1-ts_hcDBP1 (NSY73)
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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 SC medium (maintaining selection for plasmids as needed) 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 a freezer mill.
Ribosome profiling (Rnase I footprinting, size selection, RNA extraction, preadenylated linker ligation, reverse transcription, cDNA circularization, PCR amplification) was done as described in 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 2500 |
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| Description |
mRNA
Experiment 3
ded1ts_hcDBP1_37deg.csv
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| Data processing |
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
rRNA alignment with Bowtie2-2.6.0
Transcriptome alignment with TopHat v2.1.0
Read quantitation using custom scripts
Analysis of reads using DESeq2
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 |
Feb 28, 2018 |
| Last update date |
Mar 01, 2018 |
| 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 |
GPL17342 |
| Series (1) |
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| Relations |
| BioSample |
SAMN08623640 |
| SRA |
SRX3751814 |
| 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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