|
| Status |
Public on Jan 23, 2015 |
| Title |
ies2_AR005 |
| Sample type |
SRA |
| |
|
| Source name |
BY4741 Background
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741 Background
genotype: ies2Δ
|
| Treatment protocol |
none
|
| 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. For ChIP-Seq, Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries of mRNA were prepared with Illumina TruSeq RNA Sample Prep Kits v2 following the manufacturer’s protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Fastq files were used to map reads to yeast genome(saccer3) with TopHat v2.0.8 or Bowtie
Caclutate FPKM using accepted bam file from cuffdiff cuffdiff v2.0.2 for mRNA-Seq
mapped reads(sam file) were used to cacullate the mRNA level and log2 ratio of mutants vs WT using customed script
log2 ratio of mutants vs wt were used to plot with metagene profiles.
Genome_build: sacCer3_2011
Supplementary_files_format_and_content: see README file
|
| |
|
| Submission date |
Jan 23, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Siavash K Kurdistani |
| E-mail(s) |
[email protected]
|
| 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 |
GPL13821 |
| Series (1) |
| GSE52000 |
The Ino80 complex prevents invasion of euchromatin into silent chromatin |
|
| Relations |
| BioSample |
SAMN03292418 |
| SRA |
SRX851833 |
