|
| Status |
Public on Feb 12, 2009 |
| Title |
Footprints-starved-1 |
| Sample type |
SRA |
| |
|
| Source name |
yeast BY4741, 20 min amino acid starved
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
BY4741 (leu2D0 ura3D0 met15D0 his3D1)
|
| Treatment protocol |
All samples were treated for 2 min with cycloheximide 100 ug / ml
|
| Growth protocol |
Yeast strain BY4741 (leu2D0 ura3D0 met15D0 his3D1) was grown at 30 C in YEPD to OD600 = 0.6-0.7, then 20 min into minimal media w/o amino acids at 30 C if indicated
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Footprints: cells were rapidly harvested, flash-frozen in polysome lysis buffer, and pulverized in a mixer mill, extracts were digested with 150 U Rnase I for 1 hour, monosomes were purified by sucrose density gradient, RNA was extracted from the monosome fraction by hot acid phenol; total RNA was prepared from flash-frozen cells by the hot acid phenol protocol, polyA RNA was purified by oligo-dT DynaBeads, and fragmented at 95 C under mild alkali conditions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Small RNA sequencing by polyadenylation and circularization: RNA fragments were dephosphorylated, purified by filtration followed by gel purification for ~30 bp fragments, tailed with poly-A polymerase, reverse transcribed with anchored oligo-dT primer, cDNA was circularized
Footprints: sucrose density gradient; mRNA: polyA
|
| Data processing |
Reads aligned to reference genome by first 21 nt, then extended to account for the poly-A tail
|
| |
|
| Submission date |
Nov 26, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Nicholas T Ingolia |
| E-mail(s) |
ingolia@berkeley.edu, nick@ingolia.org
|
| Phone |
510 664 7071
|
| Organization name |
University of California, Berkeley
|
| Department |
Molecular and Cell Biology
|
| Lab |
Ingolia
|
| Street address |
1 Barker Hall # 3202
|
| City |
Berkeley |
| State/province |
CA |
| ZIP/Postal code |
94720 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (1) |
| GSE13750 |
Genome-Wide Analysis In Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling |
|
| Relations |
| SRA |
SRX003184 |
| BioSample |
SAMN02195616 |
