|
| Status |
Public on Sep 20, 2019 |
| Title |
WT_PlusZn_repeat2 |
| Sample type |
SRA |
| |
|
| Source name |
cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype: wild type
zn supplementation: yes
|
| Growth protocol |
wild-type and loz1 deletion strains were grown in zinc-limited EMM supplemented with 100 mM Zn to an OD600 of ~6.0
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RiboPureTM RNA Purification Kit for yeast (ThermoFisher Scientific) according to the manufacturer's instructions
Library preparation and next generation sequencing performed by Beckman Coulter Genomics. RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Splice sites generated using HISAT2 and 'Schizosaccharomyces_pombe.ASM294v2.39.gtf' from Ensembl
Sequenced reads mapped to the S.pombe genome with parameter --dta-cufflinks
Using Samtools, converted SAM files to BAM files, and sorted them based on coordinates
FPKM values for each sample was generated using Cufflinks
Cuffdiff was used to compare gene expression across samples
Genome_build: Schizosaccharomyces_pombe.ASM294v2
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
May 07, 2019 |
| Last update date |
Sep 23, 2019 |
| Contact name |
Stevin Wilson |
| E-mail(s) |
wilson.3273@osu.edu
|
| Organization name |
The Ohio State University
|
| Department |
Molecular Genetics
|
| Street address |
1787 Neil Ave, 063
|
| City |
Columbus |
| State/province |
Ohio |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL13988 |
| Series (2) |
| GSE130845 |
The zinc-responsive repressor Loz1 is the master regulator of zinc homeostasis in Schizosaccharomyces pombe [RNA-seq] |
| GSE130846 |
The zinc-responsive repressor Loz1 is the master regulator of zinc homeostasis in Schizosaccharomyces pombe |
|
| Relations |
| BioSample |
SAMN11587732 |
| SRA |
SRX5802993 |
