NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1823700 Query DataSets for GSM1823700
Status Public on Oct 07, 2015
Title wt small RNA seq
Sample type SRA
 
Source name wt S. pombe cells
Organism Schizosaccharomyces pombe
Characteristics strain: spb342
genotype/variation: wt
stain details: h90 mat3M(EcoRV)::gfp+::natMX ura4-DS/E leu1-32 ade6-M210
molecule subtype: small RNA (18 - 28 nt)
Growth protocol Fission Yeast strains were grown in standard YES medium in shaking flasks to OD ~0.5
Extracted molecule total RNA
Extraction protocol Cells were pelleted by centrifugation, washed with PBS and then total RNA was isolated using the hot phenol method. This was followed by enrichment and gel purification of small RNAs as described in Keller et al. (Nat. Struct. Mol. Biol., 2013 vol. 20 (8) pp. 994-1000)
Libraries were constructed using the Illumina TruSeq Small RNA Library Prep Kit starting with 1ug total RNA as input.
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Data processing All samples were sequenced (together with other libraries) on one lane of an HiSeq 2000 instrument. Individual reads were assigned to their sample based on the TruSeq barcode. Illumina software Casava v 1.8 was used. The 3' adapter was removed by aligning it to the read allowing one or two mismatches in prefix alignments of at least 7 or 10 bases respectively. Low complexity reads were filtered out based on their dinucleotide entropy (removing <1% of the reads). All the reads that were shorter than 14 nucleotides were removed.
Alignments to the S. pombe genome (May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/) were performed for the minus strand by the software bowtie (version 0.9.9.1) ( Langmead et al., 2009) with parameters -v 2 -a -m 100, tracking up to 100 best alignment positions per query and allowing at most two mismatches. Alignments were normalized for the size of the each library, transformed into log2 scale and corrected with a pseudocount of 3. Annotations were used as described in Woolcock et al., Genes Devc 2012, PMID: 22431512
Genomic read coverage plots were made created separately for the plus (wiggle files with _p_) and minus (wiggle files with _m_) strand, transformed into log2 scale and normalized for the size of each library based on weights of the alignments
Genome_build: May 8, 2009, http://www.sanger.ac.uk/Projects/S_pombe/
 
Submission date Jul 15, 2015
Last update date May 15, 2019
Contact name Tim Roloff
E-mail(s) tim.roloff@fmi.ch
Organization name FMI
Department Functional Genomics
Street address Maulbeerstrasse 66
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL13988
Series (2)
GSE70945 Small RNA profiles in wt and swi6 deletion strains
GSE70946 H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein
Relations
BioSample SAMN03861501
SRA SRX1097983

Supplementary file Size Download File type/resource
GSM1823700_HRH_1965_01_minus_noLog_chrElm.wig.gz 6.8 Mb (ftp)(http) WIG
GSM1823700_HRH_1965_01_plus_noLog_chrElm.wig.gz 6.7 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap