|
| Status |
Public on Nov 01, 2021 |
| Title |
RNA-seq_Control_t4 |
| Sample type |
SRA |
| |
|
| Source name |
cultured cells
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: UKY412
time point (hrs): 4
|
| Treatment protocol |
For time-course experiments, cells were initially inoculated in 5ml YPG liquid media and cultured at 30C. Logarithmically growing cells were then transferred and diluted into larger 1-1.5L YPG cultures for growth overnight at 30C while shaking in containers with 4x equivalent free-air volume. The following morning, mid-log phase cells (OD600 ~0.6-1.2) were collected by centrifugation, washed 2x within 5 minutes with ~250-500ml YP dextrose (YPD), and re-suspended in equivalent volume of YPD media for 0, 2, and 4 hours of continued growth at 30C.
|
| Growth protocol |
H4 shutoff (UKY403) and isogenic control (UKY412) strains of S. cerevisiae were obtained from the Grunstein lab. Cells were maintained on agar plates containing YPG media (1% yeast extract, 2% peptone, 2% galactose).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol Reagent following standard protocols. RNA was further purified using the RNEasy Mini Kit with on-column DNase digestion (Qiagen). Quality of extracted RNA was confirmed using an Agilent Bioanalyzer and samples with RIN > 8 were selected for sequencing. RNA from biological replicates for each control time-point and three biological replicates for each experimental (H4 Shutoff) time-point were collected.
RNA-seq was performed on all samples using the standard illumina protocol, which includes cDNA synthesis via random priming and ribosomal RNA depletion.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
RNA-seq during control histone H4 shutoff
|
| Data processing |
TopHat VN:1.4.1 sgd_r64/SacCer3 (genes.gtf from iGenomes build)
Genome_build: SacCer3
Supplementary_files_format_and_content: Bam Files where generated with Tophat (vn 1.4.1)
Supplementary_files_format_and_content: Abundance measurments contain FPKM measurements generated with cuffdiff VN:2.1.1 with saccer3 gene annotations
|
| |
|
| Submission date |
Nov 29, 2016 |
| Last update date |
Nov 01, 2021 |
| Contact name |
Michael Buck |
| E-mail(s) |
mjbuck@buffalo.edu
|
| Phone |
7168817569
|
| Organization name |
SUNY at Buffalo
|
| Department |
Biochemistry
|
| Street address |
701 Ellicott St
|
| City |
Buffalo |
| State/province |
NY |
| ZIP/Postal code |
14203 |
| Country |
USA |
| |
|
| Platform ID |
GPL9377 |
| Series (2) |
| GSE90669 |
Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription [RNA-seq] |
| GSE92468 |
Nucleosomes inhibit intragenic binding of Rap1p and subsequent cryptic transcription |
|
| Relations |
| BioSample |
SAMN06145901 |
| SRA |
SRX2426621 |
