 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 06, 2013 |
| Title |
ypd_bio2_lib1 |
| Sample type |
SRA |
| |
|
| Source name |
ypd_bio2_lib1
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: SLS045 (diploid, S288c background)
media: YPAD media
cell type: mid-log phase cells, OD 1
genotype/variation: WT
|
| Growth protocol |
Yeast cells were grown to mid-log phase (OD1) using either YPAD (1% yeast extract, 2% peptone, 1% glucose) or YPGal (1% yeast extract, 2% peptone, 1% galactose).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated by a standard hot phenol method and contaminant DNA was removed by DNase I treatment. The sample was subject to TIF-Seq protocol (Transcript IsoForm Sequencing) for the unambiguous identification of overlapping transcripts by sequencing both 5’ and 3’ ends of the each mRNA molecule. Briefly, full-length cDNA molecules for capped and polyadenylated mRNAs is produced. After that, they are subject to intramolecular ligation, fragmentation and capture of the 5’-3’ junctions. Finally paired end sequencing of those tags give information to reconstruct the transcriptome architecture.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 2
|
| Data processing |
Library strategy: TIF-Seq
Base-calling was performed using Illumina CASAVA pipeline and standard parameters.
5' and 3' sequences were extracted from paired-end sequences
5' and 3' sequences were aligned to the S288c reference R64 genome assembly using novoalign V2.07.10 with default parameters
Transcript isoforms (TIFs) were identified by exact identical 5' and 3' positions
Genome_build: Saccharomyces cerevisiae S288C reference genome R64 downloaded from SGD (http://www.yeastgenome.org/)
Supplementary_files_format_and_content: tab-delimited text files include number of TIFs of each sample (abundance measurements)
|
| |
|
| Submission date |
Jul 05, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Wu Wei |
| E-mail(s) |
wuwei@embl.de
|
| Organization name |
EMBL Heidelberg
|
| Department |
Genome Biology Unit
|
| Lab |
Steinmetz Lab
|
| Street address |
EMBL Heidelberg,Meyerhofstraße 1
|
| City |
Heidelberg |
| ZIP/Postal code |
69117 |
| Country |
Germany |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE39128 |
Saccharomyces cerevisiae Transcript Isoform mapping |
|
| Relations |
| SRA |
SRX157934 |
| BioSample |
SAMN01085929 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
|
|
|
|
 |
