|
| Status |
Public on Dec 19, 2016 |
| Title |
3xFlag-Ago1 WT (spy797) |
| Sample type |
SRA |
| |
|
| Source name |
3xFlag-Ago1 WT (spy797)
|
| 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 |
SAMN05163254 |
| SRA |
SRX1792420 |
