|
| Status |
Public on Jun 25, 2024 |
| Title |
RNAseq of parental strain, 4h with NSF, experiment 2, rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
S. pombe cell culture
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
tissue: S. pombe cell culture
strain: ED668
genotype: h+ orfdelta::ade6-M216 ura4-D18 leu1-32
treatment: 4h NSF
|
| Treatment protocol |
2, 4, 6 h growth at low density (OD=0.01) either with NSF or MeOH as control.
|
| Growth protocol |
S. pombe cell cultures were grown in standard YES medium (OD = 1, exponential phase) at 30 degrees celsius. At time point 0, cells were diluted to OD = 0.01 and shifted to EMM(187mM NH4Cl) with MeOH or NSF at 30 degrees celsius.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with the MasterPure RNA Purification Kit from epicenter (MPY03100).
Total RNA libraries were prepared with TruSeq Stranded Total RNA kit (Illumina, 20020599) according to manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw data were demultiplexed and converted to fastq format using bcl2fastq2 (v1.17) Illumina. Fastq files were aligned using STAR (v2.7.3a) with the parameters --runMode alignReads --outFilterType BySJout --outFilterMultimapNmax 100 --outFilterMismatchNoverLmax 0.05 --outSAMmultNmax 1 --outMultimapperOrder Random --outSAMtype BAM SortedByCoordinate --outSAMattributes NH HI NM MD AS nM --outSAMunmapped Within. STAR sam output was converted to bam using samtools (v1.9). Bam files were used to calculate strand-specific coverage using bedtools genomeCoverageBed (v2.27.1), resulting bedgraph files were normalized to 1 million genome mapping reads (RPM), and converted to bigWig format using bedGraphToBigWig (v4).
Assembly: Spombe.ASM294v2.24
Supplementary files format and content: bigWig files containing normalized read counts (to 1 mio genome mapping reads per library) split by plus and minus strand for visualization in UCSC or IGV genome browser.
|
| |
|
| Submission date |
May 27, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Fabio Mohn |
| E-mail(s) |
fabio.mohn@fmi.ch
|
| Organization name |
Friedrich Miescher Institute for Biomedical Research
|
| Lab |
Buehler Lab
|
| Street address |
Maulbeerstrasse 66
|
| City |
Basel |
| ZIP/Postal code |
4058 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL17225 |
| Series (2) |
| GSE250093 |
Nitrogen signaling factor changes gene expression and binding of transcription factors [RNA-seq] |
| GSE250095 |
Nitrogen signaling factor changes gene expression and binding of transcription factors |
|
| Relations |
| BioSample |
SAMN41553981 |
| SRA |
SRX24713188 |
