|
| Status |
Public on Dec 05, 2016 |
| Title |
clr4D 4h (sRNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: clr4D (975 h+ clr4D::NatMX6)
treatment: N starvation
time: 4h after -N
|
| Growth protocol |
Cells grown in EMM 225ug/ml adenine/histidine/leucine/lysine/uracil (OD~1) at 32C, and were washed twice with EMM -N. Cells were resuspended in EMM -N and incubated at 32C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared as described above from which sRNAs (less than 200bp long) were size-selected using the RNAeasy Mini kit (Qiagen). Purified sRNA (20-30nt) samples were obtained by gel extraction. Gel slices were resuspended in 0.4 M sodium acetate (pH 5.2) overnight at 4oC, and sRNA were collected by ethanol precipitation.
Sequencing libraries were prepared using the Illumina TruSeq Small RNA Library Preparation kit using 25ng of sRNA.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
small RNA
|
| Data processing |
Remove adapter with Cutadapt
Map go S pombe genome with Bowtie2 2.1.0
Select reads that starts with "U"
Select reads between 18 and 25nt
Quantify the number of reads per transcript by HTSeq 0.6.1
Genome_build: S. pombe ASM294v2.22
Supplementary_files_format_and_content: Number of reads per transcript. Txt file
|
| |
|
| Submission date |
Oct 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Joh |
| E-mail(s) |
[email protected]
|
| Organization name |
Mass General Hospital
|
| Department |
Center for Cancer Research
|
| Street address |
149 13th St
|
| City |
Charlestown |
| State/province |
MA |
| ZIP/Postal code |
02129 |
| Country |
USA |
| |
|
| Platform ID |
GPL20584 |
| Series (2) |
| GSE89149 |
Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [sRNA-Seq] |
| GSE89151 |
Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs |
|
| Relations |
| BioSample |
SAMN05938958 |
| SRA |
SRX2267901 |
