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Sample GSM2446272 Query DataSets for GSM2446272
Status Public on Oct 07, 2017
Title RNAseq cut14
Sample type SRA
 
Source name cut14
Organism Schizosaccharomyces pombe
Characteristics strain: FY8027
culture condition: 36C 2hour
mutation: cut14-208
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 SAMN06208963
SRA SRX2467302

Supplementary file Size Download File type/resource
GSM2446272_RNAseq_cut14.txt.gz 30.5 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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