|
| Status |
Public on Dec 05, 2016 |
| Title |
clr4D 24h rep2 (RNA-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Cells
|
| Organism |
Schizosaccharomyces pombe |
| Characteristics |
strain: clr4D (975 h+ clr4D::NatMX6)
treatment: N starvation
time: 24h 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 |
RNA from cell pellets was extracted by the hot phenol RNA exraction method (Leeds et al 1991), and further processed with the Rneasy Mini kit (Quagen 74104) and DNaseI (Roche)
rRNA was removed by Ribo-Zero Bold rRNA Removal Kit Yeast (Illumina MRZY1306), and libraries were constructed by NEBNext Ultra Directional RNA Librayr Prep Kit for Illumina (NEB E7420L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rRNA-depleted RNA
|
| Data processing |
Map to rRNA by TopHat 2.0.8
Convert unmapped reads into fastq
Remapp to S pombe genome with TopHat 2.0.8
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 |
GPL17225 |
| Series (2) |
| GSE89145 |
Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs [RNA-Seq] |
| GSE89151 |
Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs |
|
| Relations |
| BioSample |
SAMN05938883 |
| SRA |
SRX2267849 |
