|
| Status |
Public on Aug 15, 2010 |
| Title |
NNSR no actD |
| 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; no actinomycin D
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 |
SRX022781 |
| BioSample |
SAMN00016764 |
