|
| Status |
Public on Apr 20, 2020 |
| Title |
Sample 10: Mtr4 (dAir2)_1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
tag: HISx6-TEV proteas cleavage site-protA
tissue: yeast culture
barcode name: Ac
barcode sequence: NNNGCGCAGC
|
| Treatment protocol |
Protein-RNA complexes were stabilised by in-vivo UV crosslinking.
|
| Growth protocol |
S.cerevisiae strains expressing C-terminal HTP or N-terminal FTP 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.
CRAC (as described in Delan-Forino et al, MiMB, in press) and RNA seq (Lexogen Sense mRNA kit)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina MiniSeq |
| |
|
| Description |
RNA bound to protein of interest
|
| Data processing |
Library strategy: CRAC
CRAC Demultiplexing: Reads were assigned to experimental samples using their 5' barcode sequences, and barcodes were clipped. (For the raw reads uploaded here barcodes were not clipped)
CRAC Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
CRAC Length filtered: Reads were length filtered to keep ionly reads which were containing 3' linker
CRAC 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
CRAC Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign and counts over each genomic features calculated using pyReadCounters from pyCRAC package
RNAseq Demultiplexing: Reads were indexed during library preparation and demultiplexed by the sequencing platform
RNAseq Filtering reads: Reads were trimmed using flexbar to remove the 3’-linker sequence and quality filtered.
RNAseq Reverse Complement: Reads were reverse complemented
RNAseq Sequences filtration: Low complexity sequences were filtered out before genome alignment
RNAseq Reads alignment: Reads were aligned to the sacCer3 Saccharomyces cerevisiae genome sequence (Saccharomyces Genome Database) by novoalign, all reads mapping to non RNA polymerase II transcripts were filtered out, 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 gff format
|
| |
|
| Submission date |
Aug 07, 2019 |
| Last update date |
Apr 21, 2020 |
| Contact name |
Clementine Delan-Forino |
| E-mail(s) |
clementine.delanforino@gmail.com
|
| 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 |
GPL22715 |
| Series (1) |
| GSE135526 |
Substrate Specificity of the TRAMP Nuclear Surveillance Complexes |
|
| Relations |
| BioSample |
SAMN12527180 |
| SRA |
SRX6669864 |
