|
| Status |
Public on Sep 28, 2024 |
| Title |
PRO_BUR1-IS_ctrl_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Bur1p-IS
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: Bur1p-IS
sample group: PRO_BUR1-IS_ctrl
|
| Treatment protocol |
1mM auxin (3'-IAA) was treated to every AID strain. Final 20uM CMK was treated for inhibiting kinase activity in IS strains.
|
| Growth protocol |
Yeast cells were grown in YPD medium and harvested in mid-log phase.
|
| Extracted molecule |
other |
| Extraction protocol |
Nuclear run-on reactions and RNA extractions were performed based on the published protocol (Mahat et al., 2016) and minor conditions are altered as our previous study (Cheon et al., 2021).
Libraries were generated using the published PRO-seq or PRO-cap protocol (Mahat et al., 2016) from RNA fragmentation by base hydrolysis to full-scale PCR amplification. Minor variations in reagents were present, as previously reported (Cheon et al., 2021). To reduce the bias from PCR duplicates, we introduced the 10 nucleotides of UMI (Unique Molecular Identifier) sequences to 3’ adaptor (VRA3-UMI, 5′-/5Phos/NNNNNNNNNNGAUCGUCGGACUGUAGAACUCUGAAC/Inverted dT/−3′) of PRO-seq.
|
| |
|
| Library strategy |
OTHER |
| Library source |
other |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
PRO_BUR1-IS_ctrl_rep2
PRO-seq_BUR1-IS_DMSO_plus.bw
PRO-seq_BUR1-IS_DMSO_minus.bw
|
| Data processing |
*library strategy: PRO-seq
BigWig files were generated as previously described (Cheon et al., 2021; Booth et al., 2018) with minor modification to remove PCR duplicates using UMI-tools.
Briefly, 10-bp UMI sequences were removed and kept in the FASTQ name using the function ‘umi_tools extract’ in UMI-tools during adaptor trimming. Duplicates with the same UMI sequences were removed from the BAM files using the ‘umi_tools dedup’ function.
We simply removed UMI sequences of FASTQ and applied spike-in normalization for PRO-cap data processing.
Assembly: sacCer3, SpombeASMv2
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
May 17, 2024 |
| Last update date |
Sep 28, 2024 |
| Contact name |
Hae Jin An |
| E-mail(s) |
flora2653@kaist.ac.kr
|
| Organization name |
Korea Advanced Institute of Science and Technology
|
| Street address |
291 Daehak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL26171 |
| Series (1) |
| GSE267734 |
The Effect of Spt5p on Transcriptional Directionality [PRO-seq] |
|
| Relations |
| BioSample |
SAMN41380056 |
| SRA |
SRX24562403 |
