|
| Status |
Public on Sep 14, 2021 |
| Title |
T3 |
| Sample type |
SRA |
| |
|
| Source name |
wild type cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: 972h-
growth phase: mid-log
treatment: grown in synthetic dextrose with 8percent glucose
|
| Treatment protocol |
3%, 5% and 8% glucose added to media from the beginning
|
| Growth protocol |
Initial cell density was 5 × 104 cells/ml and cells were grown up to mid-log phase in 25 ml of medium in a 100 ml flask at 30°C with orbital shaking at 180 rpm.,
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated from mid-log cells using GeneJET RNA Purification Kit (Thermo Fisher Scientific) following the manufacturer's instructions for each sample. The purity and quantity of RNAs were measured using a Nanodrop 2000 spectrophotometer (Nanodrop Technologies, USA). Total RNAs were then used in further analysis. Three replicates were used for each sample and replicates were then pooled for sequencing according to their concentrations.
After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA(for eukaryotes). Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. The library could be sequenced using Illumina HiSeq.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
SOAPnuke software, http://soap.genomics.org.cn
BWA (Burrows-Wheeler Aligner) used for genome reference, BOWTIE used for gene reference
RSAM software
Possion Distribution method / Noiseq package / EBSeq package
http://www.yeastgenome.org/help/analyze/go-term-finder
Supplementary_files_format_and_content: xls files with FPKM values and fold change values
|
| |
|
| Submission date |
Oct 21, 2020 |
| Last update date |
Sep 14, 2021 |
| Contact name |
Ozgur Cakir |
| E-mail(s) |
[email protected]
|
| Phone |
+905555648435
|
| Organization name |
Istanbul University
|
| Street address |
Vezneciler
|
| City |
Istanbul |
| ZIP/Postal code |
34118 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL13988 |
| Series (1) |
| GSE159723 |
Transcriptome sequencing of genes related to glucose availability in Schizosaccharomyces pombe by RNA-seq analysis |
|
| Relations |
| BioSample |
SAMN16493131 |
| SRA |
SRX9322277 |
