|
| Status |
Public on Jan 11, 2017 |
| Title |
UTP23#2 |
| Sample type |
SRA |
| |
|
| Source name |
cells grown in SD (-URA/-TRP) medium
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741 (MATa; his3delta1; leu2delta0; met15delta0; ura3delta0)
tagged protein: Utp23-HTP (genomic)
|
| 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 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 Genome Analyzer IIx |
| |
|
| Description |
total cross-linked RNA
5' barcode: NNNGCGCAGC
|
| Data processing |
Library strategy: CRAC-seq
Basecalls performed using Illumina CASAVA version 1.8 (UTP23#2 and UTP23#4) or Illumina CASAVA version 1.3 (no tag)
CRAC reads were mapped to the sacCer2 genome with Novoalign, using the following settings:-F STDFQ -aTGGAATTCTCGGGTGCCAAGG -f XXX_clipped_qf.fastq -r Random -h 150 -s > XXX.novo (except sample no tag for which -F ILMFQ was used)
Genome_build: SacCer2 (SGD)
Supplementary_files_format_and_content: Mapped coordinates were converted to wig format using custom perl scripts
|
| |
|
| Submission date |
Sep 22, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Claudia Schneider |
| E-mail(s) |
Claudia.Schneider@ncl.ac.uk
|
| Organization name |
Newcastle University
|
| Street address |
Framlington Place
|
| City |
Newcastle upon Tyne |
| ZIP/Postal code |
NE2 4HH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13272 |
| Series (1) |
| GSE87238 |
In vivo RNA binding sites of the yeast ribosome biogenesis factor Utp23 |
|
| Relations |
| BioSample |
SAMN05805979 |
| SRA |
SRX2185514 |
