|
| Status |
Public on Aug 15, 2010 |
| Title |
NNSR |
| Sample type |
SRA |
| |
|
| Source name |
Yeast grown in liquid culture
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
strain: BY4741
growth stage: Mid-log
|
| Growth protocol |
Cells were grown at 30 C in a shaking water bath (New Brunswick Scientific) in the following medium: 1.5% yeast extract, 1% peptone, 2% dextrose, 0.2% SC amino acid mix (Sunrise Science). Cells were then harvested by freezing in liquid nitrogen, spun 5 minutes , 3700 x g in a Sorvall Legend RT to pellet the cells, and resuspended in 2 ml RNAlater (Ambion).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Library construction: “Not-Not-So-Random” primer protocol (‘NNSR’), where we modified the original Not-So-Random (NSR) method (Armour et al. 2009 Nature Methods) by replacing the “not so random” primers for cDNA synthesis with random (or “not not so random”) primers
RNA was extracted with the RNeasy kit (Qiagen) and treated with Turbo DNase (Ambion). Polyadenylated RNA was selected with the MicroPoly(A)Purist kit (Ambion).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
We used Arachne to map the reads to the genome. Reads in single end libraries were mapped uniquely, allowing up to 4 mismatches. Reads in paired-end libraries were first mapped non-uniquely allowing up to 4 mismatches, and then we searched for unique pairing of the non unique read mappings. A unique pairing is defined as a single pair of mappings on the same chromosome, up to 500 bp apart, with reads on opposite strands.
|
| |
|
| Submission date |
May 07, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Joshua Z Levin |
| Organization name |
Broad Institute of MIT & Harvard
|
| Street address |
320 Charles Street
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02141 |
| Country |
USA |
| |
|
| Platform ID |
GPL9377 |
| Series (1) |
| GSE21739 |
Comprehensive comparative analysis of strand-specific RNA sequencing methods |
|
| Relations |
| SRA |
SRX022780 |
| BioSample |
SAMN00016763 |
