|
| Status |
Public on Sep 25, 2012 |
| Title |
Rrp44-endo rep2 |
| Sample type |
SRA |
| |
|
| Source name |
cells grown in SD (-LEU/-TRP) medium
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: MATa; his3-delta-1; leu2-delta-0; lys2-delta-0; ura3-delta-0; rrp44-delta::kanMX6
tagged protein: Rrp44-endo-HTP (pRS315)
|
| Treatment protocol |
To generate RNA-protein crosslinks, actively growing yeast cell cultures in SD medium were UV-irradiated in a 1.2 m metal tube (“Megatron”) for 100 sec at 254 nm (according to Granneman et al., EMBO J., 2011).
|
| Growth protocol |
Yeast cell cultures were grown in SD medium (OD600 ~0.5).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extracts from UV-crosslinked yeast cells were used to isolate RNAs cross-linked to a tagged protein in a 2-step purification protocol. Recovered RNAs are subjected to limited RNAse digest, linker ligation and cDNA amplification, and identified by Illumina sequencing (according to Granneman et al., PNAS, 2009).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
5' barcode: none
|
| Data processing |
Basecalls performed using Illumina CASAVA version 1.3, except for Sample 8 (Rrp44-endo rep2), which was analyzed with CASAVA version 1.8
CRAC reads were mapped to the sacCer2 genome with Novoalign, using the following settings: -F ILMFQ -aTGGAATTCTCGGGTGCCAAGG -r Random -h 150 -s (except Sample 8 for which -F STDFQ was used)
Genome_build: SacCer2 (SGD)
Supplementary_files_format_and_content: Mapped coordinates were converted to wig format using custom perl scripts
|
| |
|
| Submission date |
Aug 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Grzegorz Kudla |
| E-mail(s) |
[email protected]
|
| Phone |
+44 (0) 131 332 2471
|
| Organization name |
University of Edinburgh
|
| Department |
MRC HGU
|
| Street address |
Crewe Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH4 2XU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE40046 |
Transcriptome-wide Analysis of Exosome Targets in the Budding Yeast Saccharomyces cerevisiae |
|
| Relations |
| SRA |
SRX176079 |
| BioSample |
SAMN01112635 |
