|
| Status |
Public on Mar 12, 2016 |
| Title |
RNA-Seq of ume6 deletion (with Chd1-Ume6) |
| Sample type |
SRA |
| |
|
| Source name |
RNA-Seq of ume6 deletion (with Chd1-Ume6)
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain background: W303
genotype/variation: ume6 deletion (with Chd1-Ume6)
isolate number: isolate 1
presence of chd1-ume6 fusion: yes
|
| Growth protocol |
cells were grown to OD600 0.4 to 0.6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with hot acid phenol, treated with Dnase I, and depleted of rRNA
Strand-specific libraries were prepared according to dUTP method and TruSeq (Illumina) Sample Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Basecalling was performed by Illumina CASAVA software package
Reads were mapped to S. cerevisiae genome (Saccharomyces_cerevisiae.EF4.65.dna.toplevel.fa) appended with ERCC Spike-in Control reads (https://tools.lifetechnologies.com/content/sfs/manuals/ERCC92.zip) using TopHat2
Mapped reads were filtered using SAMtools flags -f 3 -F 256
Differential transcript analysis was performed using CuffDiff (cufflinks 2.2.1) with a maskfile for rRNA and tRNA
Independent isolates were merged
Genome_build: Saccharomyces_cerevisia.EF4.65
Supplementary_files_format_and_content: Normalized FPKM Values of all Genes for Indicated Strains. The existance of a Ume6 binding motif (WNGGCGGCWW) within 500 base pairs of the associated gene is indicated by Has_Motif = yes.
|
| |
|
| Submission date |
Sep 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Jeffrey N McKnight |
| E-mail(s) |
jmcknig2@uoregon.edu
|
| Organization name |
University of Oregon
|
| Department |
Institute of Molecular Biology
|
| Lab |
McKnight Lab
|
| Street address |
1229 University of Oregon, 1318 Franklin Blvd, Rm 273 Onyx Bridge
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97408 |
| Country |
USA |
| |
|
| Platform ID |
GPL9134 |
| Series (2) |
| GSE72571 |
Sequence-Targeted Nucleosome Sliding in vivo - Transcription Profiling |
| GSE72572 |
Sequence-Targeted Nucleosome Sliding in vivo |
|
| Relations |
| BioSample |
SAMN04024971 |
| SRA |
SRX1176436 |
