|
| Status |
Public on Dec 22, 2020 |
| Title |
RNA sequencing of pir1∆ pat1-as2 diploid cells_26C_5h |
| Sample type |
SRA |
| |
|
| Source name |
cells growing in EMM with 25µM 1-NM-PP1 at 26˚C for 5h
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: pir1_delta pat1-as2 diploid cells
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Logarithmically growing pat1-as2 cells were starved in nitrogen depletion media (EMM-N) for 4-7h, then treated with 25 µM 1-NM-PP1 to triger meiosis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using MasterPure Yeast RNA purification kit (MPY03100, Lucigen) according to manufacturer's recommendation.
ScriptSeq v2 RNA-Seq Library Preparation Kit (Epicentre) or Ultra II Directional RNA Library Prep Kit for Illumina (NEB) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq Platform or Illumina NextSeq 500 platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads were quality trimmed using Trimmomatic and aligned to the Pombase v2.29 reference genome (Wood et al. 2003) using the STAR (Dobin et al. 2013) aligner and normalized to reads per million (RPM). Aligned reads were assigned to transcripts on the basis of Pombase annotations using Rsubread. DEGseq (Wang and Wang 2018) was used to compute the log2 fold-change in transcript expression between experimental strains and previously published WT grown at 30°C (Gallagher et al. 2018). Data for WT grown at 30°C can be found at GEO Omnibus accession numbers GSM2803075 and GSM2803077.
Genome_build: Pombase Schizosaccharomyces pombe asm294v2.29
Supplementary_files_format_and_content: Feature count tables from DEGseq; feature counts and bedgraphs generated by STAR and post-processed to produce uniform sampling intervals.
|
| |
|
| Submission date |
Dec 21, 2019 |
| Last update date |
Dec 05, 2022 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
|
| Organization name |
NCI
|
| Department |
LBMB
|
| Lab |
Shiv Grewal
|
| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL20584 |
| Series (2) |
| GSE142487 |
TOR targets RNA elimination machinery to govern facultative heterochromatin assembly and mitosis to meiosis developmental switch [RNA-seq] |
| GSE142488 |
TOR targets an RNA processing network to regulate facultative heterochromatin, developmental gene expression and cell proliferation |
|
| Relations |
| BioSample |
SAMN13664020 |
| SRA |
SRX7427999 |
