|
| Status |
Public on Feb 25, 2021 |
| Title |
WT 1 [re-analysis] |
| Sample type |
SRA |
| |
|
| Source name |
S. pombe cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: rpb1CTD-WT 1-18
genetic markers: h- ade6 ura4-D18 leu1–32
|
| Growth protocol |
Two biological replicates of the WT, Y1F, S2A, T4A, S7A,Y1F-S7A, S2A-S7A and T4A-S7A cultures were grown in YES (yeast extracts plus supplements) media at 30°C till they reached OD600 0.4 -0.7.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cells were harvested and RNA was isolated using the Qiagen RNeasy kit. RNA quality was assessed on a Bioanalyzer instrument (Agilent) and 1µg of total RNA was used to prepare polyA+ RNA using the Illumina TruSeq RNA sample kit .
RNA-seq libraries were prepared from polyA+ RNA using the Illumina TruSeq stranded total RNA Sample Prep Kit according to the manufacturers protocol. Indexed libraries were normalized and pooled (8 samples per lane) for paired-end sequencing performed using an Illumina HiSeq 2000 instrument at the Weill Cornell Medical College Genome Core Facility (in New York).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
This is duplicated sample record of GSM1264149 for the convenient retrieval of the complete raw data from SRA
|
| 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
Genome_build: 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 |
Nov 05, 2020 |
| Last update date |
Feb 25, 2021 |
| 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 |
GPL13988 |
| Series (1) |
| GSE160852 |
Transcriptional profiling of fission yeast RNA polymerase II CTD mutants |
|
| Relations |
| Reanalysis of |
GSM1264149 |
| BioSample |
SAMN16677966 |
| SRA |
SRX9446229 |
