|
| Status |
Public on Nov 09, 2022 |
| Title |
Rpb4-TAP input rep2 |
| Sample type |
SRA |
| |
|
| Source name |
YFN518
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: MATa his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220 (2um LEU2 RPB1) RPB4::TAP::TRP1
rip antibody: none
|
| Growth protocol |
Saccharomyces cerevisiae grown in YPD at 30°C.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RIP samples were obtained as described previously (PMID: 24569168). Briefly Flash‐frozen pellets of exponentially growing Rpb4‐TAP‐tagged cells (OD600 0.5–0.8) were mechanically lysed with glass beads using a FastPrep24 agitator. An aliquot of each cell lysate was used as an input control. Cell lysates were subjected to immunoprecipitation with Dyna M280 sheep anti‐rabbit IgG beads (Invitrogen) for 2 h at 4˚C. RNA‐protein complex was released by TEV protease cleavage of the TAP‐tag. The input and immunoprecipitated RNA were purified by phenol:chloroform:isoamyl alcohol extraction.
Libraries were constructed using 3'T-Fill protocol as previously described (PMID: 23295673)
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Base-calling was done during processing of sequencing data with the Illumina HiSeq2000
Sequencing reads were aligned using the GSNAP aligner (Wu & Watanabe, 2005).
The aligned reads were further filtered to remove potential false positive poly(A) site calls arising from internal mispriming as previously described (Wilkening et al, 2013). Poly(A) sites were assigned based on the first base of each read.
Genome_build: R64-1-1
Supplementary_files_format_and_content: Bedgraph files
|
| |
|
| Submission date |
Jun 09, 2020 |
| Last update date |
Nov 09, 2022 |
| Contact name |
Vicent Pelechano |
| E-mail(s) |
vicente.pelechano.garcia@ki.se
|
| Organization name |
ScilifeLab - Karolinska Institutet
|
| Department |
MTC
|
| Street address |
Nobels väg 16
|
| City |
Solna |
| ZIP/Postal code |
SE-17177 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL13821 |
| Series (2) |
| GSE152094 |
Rpb4 and Puf3 imprint and post-transcriptionally control stability of a common set of mRNAs in yeast |
| GSE152095 |
Rpb4 and Puf3 |
|
| Relations |
| BioSample |
SAMN15186449 |
| SRA |
SRX8508356 |
