|
| Status |
Public on Apr 07, 2020 |
| Title |
Small RNA sequencing in rrp6D cells |
| Sample type |
SRA |
| |
|
| Source name |
log. growing cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
growth stage: log. growing cells
genotype: Rrp6 Deletion
|
| Treatment protocol |
Temperature sensitive mutation of Pir2 and Cwf10 and deletion of Rrp6.
|
| Growth protocol |
Standard conditions were used for logarithmically growing cultures in rich media (YEA). Cultures were grown at 26C overnight and then shifted to 33C for 5hrs.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Small RNAs between 15 and 30 nucleotides were extracted from 17% Urea-PAGE gels and eluted using Corning Costar Spin-X columns (Sigma Aldrich) followed by ethanol precipitation.
NEBnext Small RNA Library for Illumina (NEB-E7330) was used according to the manufacturer's protocol
Libraries were analyzed using an Agilent 4200 TapeStation system (Agilent) and sequenced on the Illumina MiSeq platform.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
rrp6D smRNAseq
|
| Data processing |
Alignment was done using Novoalign (Novocraft).
Aligned reads were processed to retain 21-24 nucleotide reads and generate SGR files using a python script.
Mapped reads were normalized to total reads mapped.
Genome_build: asm294v2.28
Supplementary_files_format_and_content: SGR (The 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 |
Jul 31, 2019 |
| Last update date |
Apr 07, 2020 |
| 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) |
| GSE135160 |
Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression [smRNA-seq] |
| GSE135161 |
Cryptic introns in lncRNAs recruit conserved Pir2/ARS2 protein to promote gene repression |
|
| Relations |
| BioSample |
SAMN12404865 |
| SRA |
SRX6619819 |
