|
| Status |
Public on Oct 07, 2017 |
| Title |
RNAseq cut3 |
| Sample type |
SRA |
| |
|
| Source name |
cut3
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: SPO25
culture condition: 36C 2hour
mutation: cut3-477
|
| Growth protocol |
The fission yeast Schizosaccharomyces pombe strains were cultured in Yeast-Extract Adenine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The in situ Hi-C experiment was performed as previously reported (Rao et al. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping. Cell 159, 1665–80 (2014).) Total RNA was extracted from cells as previously described (Alfa et al. Experiments with fission yeast. (Cold Spring Harbor Laboratory Press, 1993).)
Hi-C samples were prepared for sequencing using NEBNext Multiplex Oligos for Illumina kit. RNA libraries were prepared for sequencing using NEBNext ultra NDA library prep kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Genome_build: ASM294v2.19
RNA-seq: Sequenced reads were mapped to the fission yeast reference genome (version ASM294v2.30) using STAR v2.5.2 program
RNA-seq: htseq-count 0.6.1 software was used to estimate read numbers assigned to exons, and the read numbers were normalized using the TMM method
RNA-seq: Differentially expressed genes between wild-type and cut14-208 condensin mutant cells were identified by edgeR package using the dispersion value of 0.029, which was estimated from the cut3-477 and cut14-208 condensin mutant samples treated as biological replicas
RNA-seq: FDR < 0.05 were used as a threshold to define significantly up- or down-regulated genes.
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include RPKM values for each transcript
|
| |
|
| Submission date |
Jan 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Hideki Tanizawa |
| E-mail(s) |
hidekit@uoregon.edu
|
| Organization name |
University of Oregon
|
| Department |
Institute of Molecular Biology
|
| Street address |
1370 Franklin Blvd
|
| City |
Eugene |
| State/province |
OR |
| ZIP/Postal code |
97403 |
| Country |
USA |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE93198 |
Architectural alterations of the fission yeast genome across the cell cycle |
|
| Relations |
| BioSample |
SAMN06208964 |
| SRA |
SRX2467301 |
