|
| Status |
Public on Jan 05, 2016 |
| Title |
small RNA sequencing in ∆rrp6 cells |
| Sample type |
SRA |
| |
|
| Source name |
∆rrp6 cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
genotype/variation: {delta}rrp6 mutant
growth stage: log. growing cells
|
| Treatment protocol |
dhp1-2 mutation in ∆rrp6
|
| Growth protocol |
Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were first grown at 30˚C to OD600=~0.2 and then shifted to 37˚C for 5 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the MasterPure™ Yeast RNA Purification Kit (epicentre)
21-25nt small RNAs were isolated by denaturing gel electrophoresis and after ethanol precipitation. Libraries were then constructed using the NEBNext Small RNA Library Prep Set for Illumina (NEB). Amplified DNA of 140-150bp was extracted from a 6% PAGE gel. Eluted DNA was ethanol precipitated overnight and resuspended in TE buffer.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq platform.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
sRNA ∆rrp6
small RNA
|
| Data processing |
Aligment of small RNAs; Novocraft 2.07.13
Adapters were trimmed and duplications were removed using Novoalign.
SGRs were generated from the aligned files and repeat nromalized to per million mapped reads.
Genome_build: ASM294v2 [asm294v2.28]
Supplementary_files_format_and_content: The data is uploaded as SGR file where first column denotes the chromosome, second column denotes the position on the chromosome counted from the 5' end on the + strand, and the 3rd column denotes the count (normalized to million mapped reads).
|
| |
|
| Submission date |
Nov 05, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Shiv Grewal |
| Phone |
2407607553
|
| Organization name |
NCI
|
| Department |
LBMB
|
| Lab |
Shiv Grewal
|
| Street address |
NCI bldg 37 Rm 6068 9000 Rockville Pike
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL16192 |
| Series (2) |
| GSE74739 |
A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing [sRNA-seq] |
| GSE74741 |
A conserved factor Dhp1/Rat1/Xrn2 triggers premature transcription termination and nucleates heterochromatin to promote gene silencing |
|
| Relations |
| BioSample |
SAMN04244582 |
| SRA |
SRX1421090 |
