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Status |
Public on Jun 25, 2024 |
Title |
RNAseq of parental strain, 4h with methanol, rep 2 |
Sample type |
SRA |
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Source name |
S. pombe cell culture
|
Organism |
Schizosaccharomyces pombe |
Characteristics |
tissue: S. pombe cell culture strain: ED668 genotype: h+ orf{del}::ade6-M216 ura4-D18 leu1-32 treatment: 4h MeOH
|
Treatment protocol |
2, 4, 6 h growth at low density (OD=0.01) either with NSF or MeOH as control.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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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.
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Submission date |
Dec 13, 2023 |
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 |
GPL28961 |
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 |
SAMN38811085 |
SRA |
SRX22878742 |