|
Status |
Public on Jan 27, 2024 |
Title |
pho7_24h-1 |
Sample type |
SRA |
|
|
Source name |
AGP83
|
Organism |
Schizosaccharomyces pombe |
Characteristics |
strain: AGP83 growth phase: 24 h phopshate starved culture, ePMGT(-PO4) medium growth medium: ePMGT(-PO4) medium genotype: h- pho7delta::natMX
|
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 |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
pho7_24HR_DESeq2.xlsx
|
Data processing |
Base calls from Illumina NovaSeq 6000 (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: DESeq output file
|
|
|
Submission date |
Nov 15, 2023 |
Last update date |
Jan 27, 2024 |
Contact name |
Angad Garg |
Organization name |
Memorial Sloan Kettering Cancer Center
|
Department |
Molecular Biology
|
Lab |
Stewart Shuman
|
Street address |
RRL-865 430 E 67th St.
|
City |
New York |
State/province |
New York |
ZIP/Postal code |
10065 |
Country |
USA |
|
|
Platform ID |
GPL28961 |
Series (1) |
GSE247799 |
Factors governing the transcriptome changes and chronological lifespan of fission yeast during phosphate starvation |
|
Relations |
BioSample |
SAMN38262101 |
SRA |
SRX22529431 |