 |
 |
GEO help: Mouse over screen elements for information. |
|
| 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 |
| E-mail(s) |
bchces@nus.edu.sg
|
| 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 |
|
| Relations |
| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
