|
| Status |
Public on Apr 14, 2015 |
| Title |
WT prep 3 |
| Sample type |
SRA |
| |
|
| Source name |
WT prep 3
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype/variation: wild type
|
| Treatment protocol |
NA
|
| Growth protocol |
All cells were grown to an OD600 of 0.8
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot acid phenol extraction
SOLiD Total RNA-seq Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Data processing |
Sequence reads were aligned with BFAST (v.0.7.0a) towards reference genome and junction library. Details refers to Breese and Liu, Bioinformatics, 2013, PMID: 23314324
Aligned reads were fitered with NGSUtils (Breese and Liu, Bioinformatics 2013), only unique mapped reads with no more than 2 mismatchs were kept.
Read counts were calculated with NGSUtils.
Differential expression analysis was performed using edgeR.
Genome_build: sacCer3
Supplementary_files_format_and_content: tab-delimited text file includes raw counts, log2 fold change values, p-values and FDR for all samples.
|
| |
|
| Submission date |
Apr 29, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yunlong Liu |
| E-mail(s) |
[email protected]
|
| Phone |
(317) 278-9222
|
| Organization name |
Indiana University School of Medicine
|
| Department |
Medical and Molecular Genetics
|
| Street address |
410 West 10th Street
|
| City |
Indianapolis |
| State/province |
IN |
| ZIP/Postal code |
46202 |
| Country |
USA |
| |
|
| Platform ID |
GPL18621 |
| Series (2) |
| GSE57155 |
Characterization of extended transcripts by RNA-Seq suggests that Rrp6 influences Nrd1-dependent termination |
| GSE87658 |
RNA-sequencing and ChIP-exo of wildtype and RTR1 and RRP6 deletion mutants in Saccharomyces cerevisiae reveal a role for RTR1 and RRP6 in noncoding transcript termination by Nrd1 |
|
| Relations |
| BioSample |
SAMN02740641 |
| SRA |
SRX528876 |
