|
| Status |
Public on Feb 04, 2020 |
| Title |
RGT1_ALL_Kang2020 |
| Sample type |
SRA |
| |
|
| Source name |
RGT1_ALL_Kang2020
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
genotype: sir4D
transcription factor: Rgt1p
|
| Treatment protocol |
"Calling Card" Assay performed as previously described: 1. "Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins." Wang H, Mayhew D, Chen X, Johnston M, Mitra RD. Genome Research, 2011, May 21(5):748-55. PMID 21471402. 2. "Calling Card Analysis in Budding Yeast." Mayhew D, Mitra RD. Cold Spring Harbor Protocols, 2016, Feb 1, 2016(2). PMID 26832687.
|
| Growth protocol |
The indicated yeast strain was co-transformed with a plasmid carrying the indicated transcription factor fused at the C-terminus to Sir4p and a plasmid carrying a barcoded HIS3-carrying Ty5 retrotransposon under the control of the GAL1/10 promoter. A single clone was then incubated for 3 days on selective media with galactose as the carbon source. Plates were then sequentially replica-plated to YPD (2 days), followed by SC-HIS with 5'FOA agar plates (3 days).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from all cells using standard glass bead-beating, phenol chloroform isoamyl alcohol purification, and NH4Ac ethanol protocol.
Genomc DNA was digested in three separate restriction enzyme digests (HinPI1, HpaII, and Taq-alphaI), self-ligated with T4 DNA ligase, and an inverse PCR reaction was performed to amplify genomic DNA downstream of each inserted Ty5 retrotransposon.
"Calling Card" Assay to identify in vivo genomic targets of DNA-binding factors
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina MiniSeq |
| |
|
| Description |
Calling Card Assay for in vivo Transcription Factor Binding: a retrotransposon is directed into the genome at loci bound by a given transcription factor
|
| Data processing |
Library strategy: "Calling Card" Assay
Paired-End sequence reads were filtered for presence of Read1 initial 5bp barcode followed by unique 17-mer sequence (AATTCACTACGTCAACA) and Read2 initial 8bp barcode.
The remaining sequence after the 17-mer sequence of Read1 was mapped to the 2008 S. cerevisiae reference genome (R-61-1-1) sequence using NovoAlign with default parameter settings.
Insertion position and number of reads mapping to each insertion are reported in gnashy file.
Genome_build: S288C-R61
Supplementary_files_format_and_content: gnashy: a table indicating genomic position of the retrotransposon insertion and number of reads aligning to that position
|
| |
|
| Submission date |
Feb 03, 2020 |
| Last update date |
Feb 04, 2020 |
| Contact name |
Yiming Kang |
| E-mail(s) |
[email protected]
|
| Organization name |
Washington University in St. Louis
|
| Department |
Computer Science and Engineering
|
| Street address |
1 Brookings Dr
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63130 |
| Country |
USA |
| |
|
| Platform ID |
GPL22715 |
| Series (1) |
| GSE144657 |
Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses |
|
| Relations |
| BioSample |
SAMN13973093 |
| SRA |
SRX7664448 |
