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| Status |
Public on Jan 15, 2018 |
| Title |
35S_control_1 |
| Sample type |
SRA |
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| Source name |
purified 35S pre-ribosomal RNP treated with DMSO
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| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain genotype: BY4741 with mrd1-deltaRDB5-TAP::K.I.TRP1, pGAL-HA-MRD1::URA3
5' barcode sequence: NNNNNNATCACGN
3' adapter sequence: AGATCGGAAGAGCACACG
rna type: pre-ribosomal RNA
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| Growth protocol |
S.cerevisiae strains were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) or YPG/R (YP with 2% Galactose and 2% Raffinose) at 30ºC.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Immunoprecipitations with TAP-tagged Mrd1 proteins were performed with TNM150 buffer (50 mM Tris-HCl pH 7.8, 1.5 mM MgCl2, 150 mM NaCl, 0.1% NP-40 and 5 mM b-mercaptoethanol), essentially as previously described (Granneman et al., 2009). RNA was extracted using a GTC phenol solution (4 M guanidine thiocyanate, 0.05 M Tris at pH 8.0, 0.01 M EDTA, 2% sarcosyl, 1% β-mercaptoethanol, 50% [v/v] phenol) as previously described (Sambrook, 1989).
cDNA libraries were generated from purified ribosomal RNA using an RT oligonucteotide containing random hexamers (SuperScript III, Invitrogen). 5' adapters were ligated on (CircLigase II, EpiCentre) and 3' adaptors generated during PCR amplification.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
purified 35S pre-ribosomal RNP treated with DMSO
[processed data files:]
35S_read_counts.sgr
35S_RT_stop_counts.sgr
Table S1.xlsx
GSM2219115
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| Data processing |
Library strategy: CRAC (High-throughput RNA structure probing library)
Base-calling by Illumina
Raw data processing was performed usign the pyCRAC package for processing of aligned reads and novoalign for aligning the reads. The complete pipeline is available at: https://bitbucket.org/sgrann/chemmodseqpipeline. NOTE! The 3' adapter sequences (AGATCGGAAGAGCACACG) and 5' in-read barcodes (13 nt) have NOT been removed.
Details about the dependencies of the ChemModSeq pipeline is provided on the repositories website. All dependencies need to be in the system path. To calculate the SHAPE reactivities, the CalculateSHAPE_reactivities script was used. For this the reads for the biological replicates of the 35S_control, 35S and Erb1_35S samples were merged to increase the coverage.
An R script that runs the BUM_HMM pipeline is also provided on the bitbucket repository. All the required text files to run the pipeline (RDN37-1 gtf annotation file, novoalign index file, sequence files) are available here.
The 35S DMSO and 1M7 datasets are also available from GSE83821 (Burlacu et al Nature Communication). However, in the fastq files provided here the 5' in-read barcode (13nt) has not been removed.
Genome_build: RDN37-1 gene from SGD (yeastgenome.org)
Supplementary_files_format_and_content: sgr file with read counts and supplementary table
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| Submission date |
Nov 14, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Sander Granneman |
| E-mail(s) |
[email protected]
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| Organization name |
University of Edinburgh
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| Department |
Centre for Synthetic and Systems Biology
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| Lab |
Granneman lab
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| Street address |
Mayfield Road, Kings Buildings, Waddington building, room 3.06
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| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JD |
| Country |
United Kingdom |
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| Platform ID |
GPL17342 |
| Series (1) |
| GSE106868 |
Maturation of the 90S pre-ribosome requires Mrd1 dependent U3 snoRNA and 35S pre-rRNA structural rearrangements |
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| Relations |
| Reanalysis of |
GSM2219115 |
| BioSample |
SAMN05301333 |
| SRA |
SRX3390386 |
| 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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