|
| Status |
Public on Oct 22, 2017 |
| Title |
Rpo21_Dbre5_MD_combined_ex6 |
| Sample type |
SRA |
| |
|
| Source name |
Rpo21-HTP in bre5∆ background, ubiquitinated Rpo21
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain/genotype: BY4741, RPO21-HTP, bre5delta
growth temperature (°c): 30
protein purification steps: IgG-Sepharore, GST-MD, Ni-NTA
|
| Treatment protocol |
Yeast cultures were irradiated with UV light, to fix protein-RNA interactions.
|
| Growth protocol |
S.cerevisiae strains were grown at the temperature indicated in the SAMPLES section to A600 ∼ 0.5 in synthetic medium with glucose minus tryptophan.
|
| 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 under denaturing conditions. When applicable, additional purification steps are indicated in the SAMPLES section. RNAs were partially digested.
Sequencing 3' adapter and 5' adapter were ligated while 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 (n is random nucleotide): NNNGACTTAGC
This samples has been sequenced twice in 2 illumina runs. There are 2 raw files. Sequences were combined to produce the processed files
|
| Data processing |
Library strategy: CRAC
Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped.
Filtering reads: Reads were trimmed using fastx-clipper (http://hannonlab.cshl.edu/fastx_toolkit/) to remove the 3’-linker sequence and quality filtered using using fastq_quality_trimmer and fastq_quality_filter (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign version 2.07.00.
Collapsing reads: To remove PCR duplicates, reads mapped to the same start position in the genome and sharing the same 3-nucleotide random barcode sequence were collapsed.
Genome_build: sacCer3
Supplementary_files_format_and_content: BigWig files contain information about the normalized (reads per million) coverage along the genome. Each dataset has one BigWig file for each strand.
|
| |
|
| Submission date |
Feb 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Camille Sayou |
| E-mail(s) |
[email protected]
|
| Organization name |
Wellcome Trust Centre for Cell Biology
|
| Lab |
Tollervey lab
|
| Street address |
Michael Swann Building, Max Born Crescent
|
| City |
Edinburgh |
| ZIP/Postal code |
EH9 3BF |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE94941 |
RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit [CRAC] |
| GSE94944 |
RNA polymerase II stalling at pre-mRNA splice sites is enforced by ubiquitination of the catalytic subunit |
|
| Relations |
| BioSample |
SAMN06339287 |
| SRA |
SRX2564634 |
