|
| Status |
Public on Sep 26, 2012 |
| Title |
wild-type-RNA-3hr-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
wild-type-RNA-3hr
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: YEF473A
carbon source: dextrose
time point: 3 hours
od: 0.8-1
|
| Treatment protocol |
Cells were collected by filtration using a 0.2ul filter, washed with media containing 1% yeast extract, 2% peptone, 2% dextrose, and resuspended at the intial concentration in fresh media containing 1% yeast extract, 2% peptone, 2% dextrose.
|
| Growth protocol |
Cells were grown with shaking at 30C in media containing 1% yeast extract, 2% peptone, 2% galactose and grown to an OD600 of between 0.8 and 1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the hot acidic phenol method (Xiao et al., 2003) from wildtype and H3-shutoff cells grown as previously described and transitioned to dextrose-containing media for 3 hours. RNA was cleaned up using the RNEasy Mini Kit (Qiagen 74104). Ribosomal RNA was removed using the RiboMinus system (Invitrogen K155003). Quality of RNA and absence of ribosomal RNA was confirmed by gel electrophoresis. 4.5ug of ribo-minus RNA was then fragmented at 70C for 5 minutes (Ambion AM8740) and used as input for double-strand cDNA synthesis using Invitrogen Double-Stranded cDNA synthesis kit (Invitrogen 11917-010) with random priming (Invitrogen 48190-011). The resulting cDNA was then prepared for Solexa sequencing using UNC HTSF protocol v. 2.5 for single-end, multiplex sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNA isolated following H3 depletion after 3 hours in dextrose
|
| Data processing |
RNA-seq reads from three biological replicates each of H3 shutoff and wildtype cells were mapped to the S. cerevisiae sacCer1 genome using TopHat (v. 1.1.0) and Bowtie (v. 0.12.6.0) with a maximum intron size of 1 kb. Samtools (v. 0.1.8.0) was used to determine pileups at each base in the genome.
|
| |
|
| Submission date |
May 14, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Jason D Lieb |
| E-mail(s) |
jlieb@bio.unc.edu
|
| Phone |
919-843-3228
|
| URL |
http://www.bio.unc.edu/faculty/lieb/labpages/default.shtml
|
| Organization name |
University of North Carolina at Chapel Hill
|
| Department |
Biology
|
| Lab |
Jason Lieb
|
| Street address |
203 Fordham Hall
|
| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
| |
|
| Platform ID |
GPL13272 |
| Series (2) |
| GSE29293 |
Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome [RNA_seq] |
| GSE29294 |
Effects of Histone H3 depletion on nucleosome occupancy and positioning through the S. cerevisiae genome |
|
| Relations |
| SRA |
SRX066579 |
| BioSample |
SAMN00622012 |
