|
| Status |
Public on Dec 02, 2016 |
| Title |
DCP2-delta-1 |
| Sample type |
SRA |
| |
|
| Source name |
culture grown in YEPD
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: CFY1016
background: W303
|
| Growth protocol |
Cells grown until O.D ~0.8 and harvested.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Hot phenol extraction followed by ethanol precipitation.
Illumina Tru-Seq library prep kit according to manufacturers reccomendations
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
total RNA treated with ribo zero
|
| Data processing |
Quality control with FastQC
Alignment to transcriptome and transcript quantitiation with RSEM and bowtie
Differential expression analysis using DESeq using RSEM expected count data with FDR cutoff 0.01
Genome_build: S288C_reference_genome_R64-2-1
Supplementary_files_format_and_content: normalized expression values as produced by DESeq, tab delimeted text file
|
| |
|
| Submission date |
Sep 05, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Allan Jacobson |
| E-mail(s) |
allan.jacobson@umassmed.edu
|
| Organization name |
UMASS Medical School
|
| Department |
MaPS
|
| Lab |
Jacobson
|
| Street address |
368 Plantation Street Albert Sherman Center AS8-1014
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01655 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE86428 |
A High Resolution Profile of NMD Substrates in Yeast |
|
| Relations |
| BioSample |
SAMN05729623 |
| SRA |
SRX2136136 |
