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Sample GSM946583 Query DataSets for GSM946583
Status Public on Apr 21, 2014
Title dcr1Δ, 3
Sample type SRA
 
Source name dcr1Δ
Organism Schizosaccharomyces pombe
Characteristics genotype/variation: dcr1-delta
Growth protocol S. pombe cells were grown on rich media (YES).
Extracted molecule total RNA
Extraction protocol Gel-purified Ago1-associated RNAs were incubated with 2μM pre-adenylated 3’-adaptor oligonucleotide (miRNA Cloning Linker-1 from IDT, AppCTGTAGGCACCATCAAT/ddC/), 1 U/μL RNAsin (Promega), 1 U/μL T4 ligase (Takara) in 10 μL ligation buffer without ATP at 20°C for 2h minutes. The 3´-ligation reaction was purified on a 17% gel. For the 5’-ligation, 3´-ligated products were incubated with 2 pmol 5’ adaptor oligonucleotide (GUU CAG AGU UCU ACA GUC CGA CGA UC), 1 U/μL RNAsin (Promega), 0.06 μg/μL BSA ,1 U/μL T4 ligase (Promega) in 10μL ligation buffer at 20°C for 2 hours. The ligated reaction was gel purified and used for first strand cDNA synthesis with RT oligo (ATT GAT GGT GCC TAC AG) for 1h at 44°C in 1x first strand buffer, 10mM DTT, 0.2 mM dNTP, 1 U/μL RNAsin (Promega) and Superscript III. cDNA was amplified using PCR with Illumina P5 (AAT GAT ACG GCG ACC ACC GAC AGG TTC AGA GTT CTA CAG TCC GAC GAT C) and Illumina P7 (CAA GCA GAA GAC GGC ATA CGA ATT GAT GGT GCC TAC AG ) oligos for 10-15 cycles and gel purified.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina Genome Analyzer II
 
Description schizosaccharomyces_pombe_972h_20080716
dcr1D.igv; dcr1D-minus.igv; dcr1D-plus.igv;
Data processing base calling
sRNA-seq reads were aligned to the pombe genome assembly using Novoalign version 2 with the standard settings
Reads mapping with two or fewer mismatches were retained.
Enrichments were calculated with our house scripts
Genome_build: schizosaccharomyces_pombe_972h_20080716
Supplementary_files_format_and_content: can be viewed with IGV browser
Supplementary_files_format_and_content: http://www.broad.mit.edu/igv
 
Submission date Jun 11, 2012
Last update date May 15, 2019
Contact name Mario Halic
E-mail(s) halic@genzentrum.lmu.de
Organization name Gene Center, University of Munich
Department Department of Biochemistry
Street address Feodor-Lynenstr. 25
City Munich
ZIP/Postal code 81377
Country Germany
 
Platform ID GPL9453
Series (1)
GSE38636 Argonaute and Trimmer generate Dicer-independent priRNAs and nucleate RNAi
Relations
SRA SRX153047
BioSample SAMN01047757

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

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