|
| Status |
Public on Feb 02, 2024 |
| Title |
Right bin of Sort-seq on YFP/RFP ratio with wildtype idr library, replicate-2, Ccr4 depletion |
| Sample type |
SRA |
| |
|
| Source name |
yeast
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4742
cell type: yeast
genotype: citirine-boxB, mScarlet-pp7, Ccr4::Ccr4-V5-mAID, OsTir1
treatment: 0.5 mM indole-3-acetic acid
|
| Treatment protocol |
For yeast expressing degron tagged nucleases, cells were grown in synthetic media minus uracil + 0.5 mM indole-3-acetic acid (Sigma I3750)
|
| Growth protocol |
Yeast were grown in synthetic media minus uracil for 16 hour in a custom turbidostat before being flow sorted (McGeachy 2019)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After flow sorting, RNA was extract by phenol/choloroform followed by ethanol precipitation
Libraries were prepared by constructing cDNA from total cellular mRNA using dT priming. Peptide constucts were amplifeid from cDNA with oJL090 and oJL109, followed by 2nd step amplification with indexing primers for illumina sequencing
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Adaptors were trimmed with Cutadapt (Martin 2011) and aligned to peptide library with bowtie2 (Langmead 2012).
Each amplicon count corresponding to a peptide was counted with SamTools (Li, 2009)
Assembly: Custom list of DNA sequences encoding 50 amino acid peptides
Supplementary files format and content: text file containing read counts for each peptide for each sample
Library strategy: Amplicon sequencing
|
| |
|
| Submission date |
Jan 29, 2024 |
| Last update date |
Feb 02, 2024 |
| Contact name |
Joseph Heimlich Lobel |
| E-mail(s) |
jhlobel@berkeley.edu
|
| Phone |
7324392625
|
| Organization name |
UC berkeley
|
| Department |
Molecular and Cell Biology
|
| Street address |
1 Barker Hall # 3202
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE254492 |
Defining the mechanisms and properties of post-transcriptional regulatory disordered regions by high-throughput functional profiling |
|
| Relations |
| BioSample |
SAMN39658544 |
| SRA |
SRX23430866 |
