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Sample GSM2724492 Query DataSets for GSM2724492
Status Public on Dec 06, 2017
Title WT-1
Sample type SRA
Source name Log phase cell culture
Organism Schizosaccharomyces pombe
Characteristics strain: KOR3006
Growth protocol Cells were grown in YEA media at 30°C to log phase.
Extracted molecule total RNA
Extraction protocol Cell pellets harvested from mid-log phase cultures were homogenised using glass beads (0.5 mm; BioSpec, Bartlesville, OK) and Fastprep homogenizer (MP Biomedicals, Switzerland). RNA samples were extracted using TRIzol (Thermo Scientific, Waltham, MA) and purified by phenol:chloroform:isoamyl alcohol (25:24:1) (PCI) (Nacalai Tesque, Kyoto, Japan) extraction thrice. Total RNA (50 μg) was treated with DNase I (Thermo Scientific) in the manufacturer-supplied buffer following the manufacturer’s protocol.
RNA-seq and primary data analyses were supplied by BGI (Shenzhen, China) using an Illumina HiSeqTM 2000 platform (Illumina, San Diego, CA).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Data processing Illumina GA Pipeline v1.5 used for base calling
Sequenced reads were filtered to remove reads with adaptors, reads with more than 10% unknown bases, low quality reads
Clean reads were mapped to genome reference using BWA (Li H and Durbin R, 2009) and to gene reference using Bowtie (Langmead B et al., 2009)
Gene expression level are quantified by a software package RSEM (RNASeq by Expectation Maximization). FRKM method is used in calculating expression level.
Genome_build: ASM294v2.25
Supplementary_files_format_and_content: xls files contains: gene ID number; transcript list of gene; length of gene; support reads number to this gene after model regulation; FPKM value of this gene
Submission date Aug 01, 2017
Last update date May 15, 2019
Contact name Ee Sin Chen
Organization name National University of Singapore
Department Biochemistry
Street address 8 Medical Drive, MD7 level 5
City Singapore
ZIP/Postal code 117597
Country Singapore
Platform ID GPL13988
Series (1)
GSE102125 Next generation sequencing for quantitative analysis of wild type and Y41F transcriptomes
BioSample SAMN07431737
SRA SRX3052744

Supplementary file Size Download File type/resource
GSM2724492_WT-1.gene.FPKM.xls.gz 70.6 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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