|
| Status |
Public on May 18, 2017 |
| Title |
upf1 deletion replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741/2_upf1 deletion
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: BY4741/2
genotype background: his-leu-ura-
ploidy: Haploid
genotype/variation: upf1 deletion
molecule subtype: rRNA-depleted RNA
|
| Growth protocol |
Cells were grown up to midlog phase (OD600 between 0.4-0.7) in YPDextrose.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using hot phenol extraction, treated with Roche Dnase
Library was constructed using TRUseq V2 kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
upf1_1
|
| Data processing |
Illumina CASAVA used for basecalling
Reads demultiplexed requiring exact barcode match
Paired-end reads merged
Unfiltered reads aligned using STAR v2.4.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, the number of reads falling in the exons of each transcript were counted and normalized by the size of the transcript and library.
Genome_build: saccer3
Supplementary_files_format_and_content: The processed data file is RPKM measurements for each gene in each sample
|
| |
|
| Submission date |
Apr 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen Douglass |
| Organization name |
University of California, Los Angeles
|
| Department |
Molecular, Cell and Developmental Biology
|
| Lab |
Johnson
|
| Street address |
5128 TLSB Terasaki Life Sciences Building, 610 Charles Young Drive East
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL13821 |
| Series (1) |
| GSE97416 |
The histone variant H2A.Z promotes efficient co-transcriptional splicing in S. cerevisiae |
|
| Relations |
| BioSample |
SAMN06688273 |
| SRA |
SRX2708861 |
