|
| Status |
Public on Jun 20, 2017 |
| Title |
VPS13-D716H_mmm1del |
| Sample type |
SRA |
| |
|
| Source name |
BY4741 Background
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
genotype: VPS13-D716H, mmm1-delta
|
| Growth protocol |
Yeast cells were grown in YPD to exponential phase at OD600 around 0.8-1.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with phenol, digested with DNase and further purified by Trizol
Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 or KAPA stranded mRNA-Seq Kits following the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
FPKM_VPS13D716H_20160708.xlsx
|
| Data processing |
Fastq files were used to map reads to yeast genome(saccer3) with TopHat v2.0.8, For pair-end sequencing, treat as single-end
Caclutate FPKM using accepted bam file from cuffdiff cuffdiff v2.0.2 for mRNA-Seq
log2 ratio of mutants vs wt were used
Genome_build: sacCer3
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
May 31, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
Skurdistani@mednet.ucla.edu
|
| Organization name |
UCLA
|
| Department |
Biological Chemistry
|
| Lab |
Kurdistani
|
| Street address |
615 Charles E Young Dr South
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
| |
|
| Platform ID |
GPL21656 |
| Series (1) |
| GSE99499 |
Endoplasmic reticulum–mitochondria junction is required for iron homeostasis |
|
| Relations |
| BioSample |
SAMN07180245 |
| SRA |
SRX2872520 |
