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Sample GSM2174867 Query DataSets for GSM2174867
Status Public on Dec 19, 2016
Title ura4+::priRNA1 ago1∆ + OE Flag-Ago1 WT (spy3473 + pDM817) - sRNA sense
Sample type SRA
 
Source name ura4+::priRNA1 ago1∆ + OE Flag-Ago1 WT (spy3473 + pDM817) - sRNA sense
Organism Schizosaccharomyces pombe
Characteristics media: EMM -LEU
antibody: Flag antibody (Sigma, F1804)
Growth protocol Cells were cultured overnight in EMM-LEU medium at 32°C and harvested at early log phase (OD600 = 1.2). ~0.5g of cells were used.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the mirVana kit (according to the manufacturer protocol)
Small RNA libraries were constructed as previously described (Halic and Moazed, 2010). Briefly, 21-24nt RNA was size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 3’ adapter. The ligated species were size-selected on a 17.5% polyacrylamide/7M urea gel and ligated to a 5’ adapter. RNA was then reverse transcribed into cDNA and PCR-amplified in a two-step process. Amplified cDNA was gel-purified and sequenced on an Illumina High-Seq platform.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
 
Data processing Reads were aligned to the S. pombe genome using novoalign, normalized for reads per million, and visualized using IGV.
Genome_build: ASM294v2
Supplementary_files_format_and_content: Mapped reads were normalized to reads per million and visualized in Integrated Genome Viewer (IGV) in an IGV-viewable format.
 
Submission date May 23, 2016
Last update date May 15, 2019
Contact name Nahid Iglesias
E-mail(s) nahid.iglesias@duke.edu
Phone 919-613-3385
Organization name Duke University
Department Biomedical Engineering
Lab Charles Gersbach
Street address 101 Science Drive, CIEMAS Rm. 2323
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platform ID GPL13988
Series (2)
GSE81733 Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation [ncRNA-seq 2]
GSE81734 Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation
Relations
BioSample SAMN05163255
SRA SRX1792432

Supplementary file Size Download File type/resource
GSM2174867_Ago1_WT_antisense.tdf 12.4 Mb (ftp)(http) TDF
GSM2174867_Ago1_WT_sense.tdf 12.1 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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