|
| Status |
Public on Jun 16, 2019 |
| Title |
aps1-3 |
| Sample type |
SRA |
| |
|
| Source name |
aps1∆
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
lab strain number: AS 1884
growth conditions: log phase culture, YES medium
developmental stage: vegetative growth
|
| Growth protocol |
log phase cultures, 30ºC, YES 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 HiSeq 4000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Base calls from Illumina HiSeq 4000 (FASTQ files)
Each replicate processed separately
The FASTQ files were mapped to the S. pombe genome (version: Schizosaccharomyces_pombe.ASM294v2.28) 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
Genome_build: Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa (Reference sequence, ftp://ftp.pombase.org/pombe/genome_sequence_and_features/OLD/20150909/Schizosaccharomyces_pombe.ASM294v2.28.dna.genome.fa.gz)
Supplementary_files_format_and_content: Matrix file for raw HTSeq counts; individual files for DESeq2 for comparison of each mutant with WT
|
| |
|
| Submission date |
May 15, 2019 |
| Last update date |
Jun 16, 2019 |
| 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 |
GPL22682 |
| Series (1) |
| GSE131237 |
Inositol pyrophosphate dynamics impact fission yeast phosphate homeostasis via modulation of RNA 3' processing and transcription termination |
|
| Relations |
| BioSample |
SAMN11652415 |
| SRA |
SRX5833529 |
