|
| Status |
Public on Jul 03, 2013 |
| Title |
RNA from S. cerevisiae |
| Sample type |
SRA |
| |
|
| Source name |
Saccharomyces cerevisiae
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
direct rna sequence from: Saccharomyces cerevisiae
strain: JGY2000
|
| Growth protocol |
Cells were cultured to mid-log phase in rich medium (YPD for S. cerevisiae).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by the hot acidic phenol method and purified with DNase treatment on Qiagen RNeasy columns.
RNA sequenced directly by Helicos (DRS method); purified RNA was not modified
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
For this Sample, the rawest possible data file is not available. It is not possible to obtain the rawest form of the data, as Helicos is now out of business. Helicos supplied the sequence output as an aligned txt file, JGY2000_fc1.ch01.filtered.txt.gz (linked below as a supplementary file). It is the most unmanipulated form of the data and contains the raw reads.
Note: GSM1154250 raw data file is identical to GSM1262423 raw data file.
|
| Data processing |
alignment to genome (Helicos Helisphere)
separation of unambiguous data by yeast species
counting of sequence tags by coordinate on each strand
classification of coordinates by associated ORF on appropriate strand
Saccharomyces cerevisiae genome build 61 (2008/06/05); D. hansenii genome release 2 (2008/09/10); K. lactis version CR382121.1 (2004/07/03)
Genome_build: Saccharomyces cerevisiae: SGD genome build 61 (2008/06/05), version S288C_reference_genome_R61-1-1_20080605.tgz; http://downloads.yeastgenome.org/sequence/S288C_reference/genome_releases/.
Genome_build: D. hansenii: ASM644v1
Genome_build: K. lactis: ASM251v1
Supplementary_files_format_and_content: Tab-delimited text files of tag counts at each coordinate in the 400 nt downstream of each ORF.
|
| |
|
| Submission date |
Jun 05, 2013 |
| Last update date |
Jun 02, 2015 |
| Contact name |
Zarmik Moqtaderi |
| Organization name |
Harvard Medical School
|
| Department |
BCMP
|
| Lab |
Struhl lab
|
| Street address |
240 Longwood Avenue C2-355
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL17245 |
| Series (1) |
| GSE47661 |
Species-specific factors mediate extensive heterogeneity of mRNA 3' ends in yeasts |
|
| Relations |
| BioSample |
SAMN02191533 |
