|
| Status |
Public on Jan 01, 2014 |
| Title |
loc1_riboProfiling |
| Sample type |
SRA |
| |
|
| Source name |
loc1- cells (BY4741 loc1::KAN)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
cell line: BY4741 loc1::KAN
treatment: Isolation of ribosome footprint RNAs
|
| Treatment protocol |
Cycloheximide was spiked into the cultures at a concentration of 100ug/ml 1 minute prior to harvesting by filtration and freezing in liquid nitrogen.
|
| Growth protocol |
Cells were grown to OD600 = 0.6 in 750ml YPD shaking at 30C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Methods are as described in Ingolia et al., 2009, except for the use of rRNA substraction for "fp" samples and linker ligation for all samples, which are described in Ingolia et al., 2011. In fastq files below, trim the 3' linker sequence "CTGTAGGCACCATCAAT" and all bases further toward the 3' end of the read.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
RNA-seq for half of the files below (file name contains "mrna"), and ribosome-footprint sequencing for the other half (file name contains "fp" for footprints)
|
| Data processing |
Reads from the fastq files were algined to the Feb 6, 2010 version of the S288C genome from SGD using bowite (http://bowtie-bio.sourceforge.net/index.shtml). Using custom software, the number of uniquely mapping reads were assigned to corresponding positions in the genome in a strand-specific manner. For degenerate reads that map to more than one position, each read was split among its mapped locations in proportion to the density of uniquely mapping reads at each location (e.g., a read mapping to two positions, where one is in a gene with 500 unique reads and the other two a gene with 250 unique reads), we incremented the number of counts at the first position by 2/3 (i.e., 500/(250+500)) and at the second position by 1/3 (i.e., 250/(250+500))). For degenerate locations outside of genes, we considered the density in a 56-nt window centered on the location.
|
| |
|
| Submission date |
Dec 14, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Suzanne Komili |
| Organization name |
Harvard University
|
| Street address |
44 Binney St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL13272 |
| Series (2) |
| GSE34438 |
Ribosome profiling of wild-type and loc1- cells in S. cerevisiae |
| GSE34534 |
Genome-wide analyses of Loc1, Puf6, and Khd1 |
|
| Relations |
| SRA |
SRX111552 |
| BioSample |
SAMN00765539 |
