|
Status |
Public on Jan 27, 2024 |
Title |
ecl123del_48h_biol_rep_1 |
Sample type |
SRA |
|
|
Source name |
yeast
|
Organism |
Schizosaccharomyces pombe |
Characteristics |
lab strain number: ASY136 growth conditions: 48h phosphate starved culture, ePMGT(-PO4) medium cell type: yeast genotype: ecl1, ecl2, ecl3 knockout
|
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
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Description |
h- ecl1∆::hygMX ecl2∆::natMX ecl3∆::kanMX
|
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 Supplementary files format and content: DESeq2 output file
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|
|
Submission date |
Nov 15, 2023 |
Last update date |
Jan 27, 2024 |
Contact name |
Ana M Sanchez |
E-mail(s) |
sanchea6@mskcc.org
|
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) |
GSE247922 |
Factors governing the transcriptome changes and chronological lifespan of fission yeast during phosphate starvation I |
|
Relations |
BioSample |
SAMN38270668 |
SRA |
SRX22539666 |