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Status |
Public on Dec 06, 2017 |
Title |
Y41F-2 |
Sample type |
SRA |
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Source name |
Log phase cell culture
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Organism |
Schizosaccharomyces pombe |
Characteristics |
strain: SPBB298
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Growth protocol |
Cells were grown in YEA media at 30°C to log phase.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Aug 01, 2017 |
Last update date |
May 15, 2019 |
Contact name |
Ee Sin Chen |
E-mail(s) |
bchces@nus.edu.sg
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Organization name |
National University of Singapore
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Department |
Biochemistry
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Street address |
8 Medical Drive, MD7 level 5
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City |
Singapore |
ZIP/Postal code |
117597 |
Country |
Singapore |
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Platform ID |
GPL13988 |
Series (1) |
GSE102125 |
Next generation sequencing for quantitative analysis of wild type and Y41F transcriptomes |
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Relations |
BioSample |
SAMN07431734 |
SRA |
SRX3052747 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2724495_Y41F-2.gene.FPKM.xls.gz |
70.9 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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