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Sample GSM2174865 Query DataSets for GSM2174865
Status Public on Dec 19, 2016
Title Untagged WT (spy137)
Sample type SRA
 
Source name Untagged WT (spy137)
Organism Schizosaccharomyces pombe
Characteristics media: EMM -LEU
antibody: Flag antibody (Sigma, F1804)
Growth protocol Cells were cultured overnight in YES medium at 32°C and harvested at early log phase (OD600 = 0.8). ~5g of cells were used.
Extracted molecule total RNA
Extraction protocol Nuclei were isolated and sRNA associated with Ago1 were immunoprecipitated with Flag antibody
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)
GSE81732 Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation [ncRNA-seq 1]
GSE81734 Distinct Functions of Argonaute Slicer in siRNA Maturation and Heterochromatin Formation
Relations
BioSample SAMN05163253
SRA SRX1792419

Supplementary file Size Download File type/resource
GSM2174865_UNTAGGED_antisense.tdf 30.9 Mb (ftp)(http) TDF
GSM2174865_UNTAGGED_sense.tdf 30.7 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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