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Sample GSM2304879 Query DataSets for GSM2304879
Status Public on Aug 22, 2017
Title control 3
Sample type SRA
 
Source name wild type, vector
Organism Schizosaccharomyces pombe
Characteristics genotype: wild type
Growth protocol Growth at 29 C in EMM2 media.
Extracted molecule total RNA
Extraction protocol Hot phenol total RNA extraction
Library construction protocol not provided.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing BGI basecalling
Trimmomatic v0.32 (PE) used for adapter trimming with parameters: ILLUMINACLIP:./TruSeq3-PE-2.fa:2:30:10:8:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:0
Reads were aligned to the pombe genome with STAR v.2.3.0e with standard parameters except: MismatchNoverLmax=0.1, MismatchNmax=3, MatchNmin=18
Gene annotations in gtf format was downloaded from PomBase version 38 from October 2013
Gene count.txts based on the PomBase annotation were obtained from each STAR alignment file using htseq-count.txt with mode=union.
Genome_build: pombe.ASM294v2.21
Supplementary_files_format_and_content: Tab-delimited text files of raw ht-seq count.txt output
 
Submission date Sep 07, 2016
Last update date May 15, 2019
Contact name Rasmus Hartmann-Petersen
Organization name University of Copenhagen
Department Department of Biology
Lab Section for Biomolecular Sciences
Street address Ole Maaloes Vej 5
City Copenhagen
ZIP/Postal code 2200N
Country Denmark
 
Platform ID GPL13988
Series (1)
GSE86512 Bag101 overexpression in S. pombe
Relations
BioSample SAMN05736232
SRA SRX2144117

Supplementary file Size Download File type/resource
GSM2304879_Control_3_union.count.txt.gz 29.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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