|
| Status |
Public on Mar 20, 2017 |
| Title |
Rrp44-HTP_Rrp41-channel_2 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741-Rrp44-HTP_Rrp41-channel_2
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cleavage site: HISx6-TEV proteas cleavage site-protA
strain: BY4741
tagged protein: Rrp44-HTP
|
| Treatment protocol |
Protein-RNA complexes were stabilised by in-vivo UV crosslinking.
|
| Growth protocol |
S.cerevisiae strains expressing C-terminal HTP tagged proteins were grown at 30°C to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
UV stabilized protein-RNA interactions were purified under denaturing conditions and RNAs associated with HTP-tagged protein were partially truncated.
Sequencing 3' adapter and 5' adapter were ligated while HTP-protein-RNA complexes were bound to Ni-NTA agarose, RNA library was reverse transcribed and PCR amplified.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
barcode: NNNCACTAGC
|
| Data processing |
Library strategy: CRAC-seq
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
Collapsing reads: To remove PCR duplicates, reads with the same start and end and sharing the same 3-nucleotide random barcode sequence were collapsed using pyRemoveDuplicate.py from pyCRAC package
Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign version 2.07.00 and counts over each genomic features calculated using pyReadCounters from pyCRAC package
Genome_build: sacCer3
Supplementary_files_format_and_content: Counts over genomic features of mapped reads in gtf format
|
| |
|
| Submission date |
Nov 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Clementine Delan-Forino |
| E-mail(s) |
[email protected]
|
| Phone |
01316507093
|
| Organization name |
University of Edinburgh - WTCCB
|
| Lab |
Tollervey lab
|
| Street address |
Michael Swann Building 5.1, King's Buildings, Mayfield Road
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3JR |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE90647 |
Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex |
|
| Relations |
| BioSample |
SAMN06067887 |
| SRA |
SRX2589419 |
