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Sample GSM1902809 Query DataSets for GSM1902809
Status Public on Jan 01, 2016
Title Rrp6 B
Sample type SRA
 
Source name rrp6∆
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: knock out of rrp6 gene
Treatment protocol 30 degrees, harvested during logaritmic phase, O.D. 0,5 - 1
Growth protocol YEA liquid medium - Yeast Extract + Casaminacids + Adenine + Glucose
Extracted molecule total RNA
Extraction protocol Hot Phenol RNA extraction, Qiagen RNA-easy clean up
Poly-A enrichment using oligo(dT) beads. cDNA synthesis using Invitrogen Supercript III. Incorporation of dUTP on second strand. Standard Illumina library preparation protocol.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description h- Leu1-32 His2 Ura4 DS/E 216 rrp6∆::KanMx6 Otr1R(Sph1)::ura+
Data processing Qualitycontrolled, filtered and trimmed using FASTX-Toolkit Hannon Lab
Aligment against S. Pombe genome EF2 using Bowtie 0.12.7
Differential Expression using DEseq
Genome_build: S. Pombe EF2
Supplementary_files_format_and_content: Microsoft Excel, Differential expression data with baseMeanA as wt control and baseMeanB as corresponding mutant strain.
 
Submission date Oct 06, 2015
Last update date May 15, 2019
Contact name Jonas Carlsten
E-mail(s) jonas.carlsten@gu.se
Organization name University of Gothenburg
Department Biomedicin
Lab Claes Gustafsson
Street address Medicinaregatan 9A
City Göteborg
ZIP/Postal code 413 91
Country Sweden
 
Platform ID GPL13988
Series (1)
GSE73792 Comparison of RNA profiling between wild type, med20∆, rrp6∆ and med20∆/rrp6∆ in Schizosaccharomyces pombe
Relations
BioSample SAMN04147858
SRA SRX1309148

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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