|
| Status |
Public on Jun 25, 2020 |
| Title |
yeast unselected 40S 1-2 |
| Sample type |
SRA |
| |
|
| Source name |
cell culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: H25 (eIF3c/NIP1-FLAG)
rna fragment size selection: approximately 18 to 85
co-ip: no
protocol: RNA 40S footprint
|
| Treatment protocol |
incubation of the cell culture with 0.8 % w/v formaldehyde on ice for 1 h
|
| Growth protocol |
in 1 litre YPD at 30ºC up to OD600 of ~0.7-0.8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cell lysis with bead beater, RNase I digestion to generate ribosomal footprints, 40S/80S separation (followed by Co-IP if indicated), hot acid phenol RNA extraction
library construction according to Ingolia et al., 2010, Methods Enzymol (different RNA fragment size selection, different set of rRNA depletion oligos)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: TCP-seq
Illumina CASAVA 1.8 for base calling
adapter trimming (fastx_clipper of FASTX Toolkit 0.0.13), filtering by alignment to rRNA (bowtie 1.2.2) and ncRNA, tRNA (bowtie2 2.2.6)
alignment to transcriptome Ensembl R64-1-1.80 (with 3’ UTR, 5’ UTR, and 5’ UTR intron annotation from SGD) and genome R64-1-1 with TopHat 2.1.0
Genome_build: R64-1-1
Supplementary_files_format_and_content: metagene_FP5end_AUG_-80+30_FPlength.tbl; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the AUG start codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: metagene_FP5end_STOP_-80+30_FPlength.tbl; counts of footprint 5’ ends positioned from -80 nt to +30 nt relative to the STOP codon (over rows) respecting the footprint length (18 – 98 nt over columns)
Supplementary_files_format_and_content: metagene_coverage_CAP_-40+40.csv; footprint coverage from -40 nt to +40 nt relative to the transcript start
Supplementary_files_format_and_content: genewise_FPcount_transcript_area.csv; footprint count per transcript area
Supplementary_files_format_and_content: genewise_mean_CI_FP5end_FP3end_AUG_-50+50.ods; distribution (mean and 95 percentiles) of footprint 5’end and 3’end positions relative to the AUG start codon of start codon associated footprints without 5’extension (footprint 5’end from -12 to -14 nt)
Supplementary_files_format_and_content: genewise_mean_CI_FP5end_FP3end_AUG_-50+50_all_AUG_associated_FPs.ods; distribution (mean and 95 percentiles) of footprint 5’end and 3’end positions relative to the AUG start codon of start codon associated footprints
Supplementary_files_format_and_content: coverage_GCN4_YEL009C_-50.csv; coverage for the 5’UTR and the beginning of the CDS for GCN4 (starting at -50 nt from the transcript start)
Supplementary_files_format_and_content: coverage_for_co-translational_assembly.ods; coverage for eIF3a, eIF3b, eIF3g and eIF2beta of 80S footprints and eIF3a/c bound 80S footprints (starting at -50 nt from transcript start)
|
| |
|
| Submission date |
Oct 20, 2019 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Susan Wagner |
| E-mail(s) |
[email protected]
|
| Organization name |
Australian National University
|
| Department |
The John Curtin School of Medical Research
|
| Lab |
RNA Biology - Preiss Group
|
| Street address |
131 Garran Road
|
| City |
Canberra |
| State/province |
ACT |
| ZIP/Postal code |
2601 |
| Country |
Australia |
| |
|
| Platform ID |
GPL17342 |
| Series (2) |
| GSE139130 |
Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes [Yeast] |
| GSE139132 |
Selective Translation Complex Profiling in yeast and human Reveals Staged Initiation and Co-translational Assembly of Initiation Factor Complexes |
|
| Relations |
| BioSample |
SAMN13065541 |
| SRA |
SRX7026363 |
