|
| Status |
Public on Dec 05, 2023 |
| Title |
STF6_biol_rep_3 (asp1) |
| Sample type |
SRA |
| |
|
| Source name |
h+ STF6 [asp1-W386*::hygMX]
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
lab strain number: BS848
growth conditions: log phase culture, ePMGT medium
developmental stage: Vegetative growth
genotype: asp1-W386*
cell type: yesat cell
|
| Growth protocol |
Log phase cultures grown at 30˚C in YES medium or ePMGT medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Hot acid phenol RNA purification protocol
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded mRNA Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled for paired-end sequencing performed using an Illumina NovaSeq 6000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
Stranded polyA+ RNA seq
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
STF6_3
count_matrix_STF.xlsx
STF6_STF9_DESeq.xlsx
|
| Data processing |
Base calls from Illumina NovaSeq 6000 or HiSeq 2000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (current version, source: Pombase) using HISAT2_2.1.0
Resulting SAM files were converted to BAM files using Samtools
Count files for individual replicates were generated with HTSeq-0.10.0 using exon annotations from Pombase (GFF annotations, genome-version ASM294v2; source ‘ensembl’)
Differential gene expression and fold change analysis was performed in DESeq2
Assembly: Schizosaccharomyces_pombe_all_chromosomes.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/genome_sequence/Schizosaccharomyces_pombe_all_chromosomes.fa.gz)
Supplementary files format and content: Matrix file for raw HTSeq counts
|
| |
|
| Submission date |
Aug 18, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Ana M Sanchez |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Molecular Biology
|
| Lab |
Stewart Shuman
|
| Street address |
430 E 67th Street, RRL-865
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL28961 |
| Series (1) |
| GSE241189 |
Genetic suppressor screen identifies Tgp1 (glycerophosphocholine transporter), Plc1 (phospholipase C), and Kcs1 (IP6 kinase) as determinants of inositol pyrophosphate toxicosis in fission yeast |
|
| Relations |
| BioSample |
SAMN37050925 |
| SRA |
SRX21415183 |
