|
| Status |
Public on Apr 25, 2014 |
| Title |
WT -GLU RNA-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
YWG25
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
poly-a selection: oligo-dT Cellulose
strain: Sigma1278b
|
| Treatment protocol |
Cells were treated with 100ug/ml cycloheximide, then harvested by centrifugation. Cell pellet was frozen in liquid nitrogen.
|
| Growth protocol |
Yeast were grown to mid-exponential phase (OD~0.7) at 30C in YPD
|
| Extracted molecule |
total RNA |
| Extraction protocol |
frozen cell pellets were thawed in lysis buffer and lysis was performed with glass beads as described in the text. Extracts were clarified by a 20' spin at 11,500 rpm in an SS-34 rotor
Footprints: 50 OD units of extract were treated with 50U of RNAse1 and subsequently purified from the monosome region of a sucrose gradient. RNA was extracted by hot acid phenol. Total RNA: RNA was extracted from 50 OD of extract by SDS and hot acid phenol, and poly(A) RNA was purified on DynaBeads. RNA was fragmented at 95C with zinc chloride
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Small RNA sequencing by polyadenylation and circularization. RNA fragments were dephosphorylated, purified by filtration then gel to isolate ~28nt fragments. Fragments were poly(A) tailed and reverse transcribed with an anchored oligo-dT primer, followed by cDNA circularization and PCR
|
| Data processing |
Reads whose 5' ends map from 12nt 3' of CDS start to 14nt 5' of CDS end are assigned to that gene (first 8 codons are omitted to avoid artifacts due to the use of cylcoheximide in library preparation)
|
| |
|
| Submission date |
Oct 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Pavanapuresan Vaidyanathan |
| E-mail(s) |
pavanapuresan@gmail.com
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Biology
|
| Lab |
Wendy Gilbert
|
| Street address |
68-341, 31 Ames Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL13272 |
| Series (1) |
| GSE51532 |
Protein Kinase A Regulates Gene-Specific Translational Adaptation in Differentiating Yeast |
|
| Relations |
| BioSample |
SAMN02380548 |
| SRA |
SRX366905 |
