|
| Status |
Public on Apr 11, 2008 |
| Title |
dcr-2_non-beta-eliminated |
| Sample type |
other |
| |
|
| Source name |
dcr-2 mutant heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
Heads were dissected from dcr-2 mutant adult flies (dcr-2^{L811fsX} allele described in Lee et al. (2004) Cell 117(1):69-81) as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).
|
| Biomaterial provider |
Megha Ghildiyal
|
| Extracted molecule |
other |
| Extraction protocol |
Total RNA was extracted using the mirVana kit (Ambion), then short (18-30 nt) RNAs were gel-purified. 2S rRNA was depleted as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).
|
| Label |
not applicable
|
| Label protocol |
not applicable
|
| |
|
| Hybridization protocol |
not applicable
|
| Scan protocol |
not applicable
|
| Description |
This RNA sample was not beta-eliminated before adapter ligation.
This sample was not used in Ghildiyal et al. (2008) Science, where a better dataset (with optimized deep-sequencing protocol) was available (GEO sample #GSM278703).
|
| Data processing |
Small RNA sequences were extracted from the deep-sequencing reads by the following procedure:
For n=29 nt, identify all the reads whose 5´ n-mer is immediately followed by the first trinucleotide (CTG) of the 3´ adapter, and whose 5´ n-mer perfectly maps on the Drosophila melanogaster genome (assembly R5.5 from FlyBase). These inserts are removed from the pool, and flagged as "29 nt-long inserts".
Decrease n iteratively (n=28 nt, n=27 nt, ...) and repeat the above procedure at each step, until n=18 nt.
Pool all 12 sets (29 nt-long inserts, 28 nt-long inserts, ..., 18 nt-long inserts), to generate the list of genome-matching inserts.
Raw data available at SRA under accession SRX000323
|
| |
|
| Submission date |
Apr 01, 2008 |
| Last update date |
May 15, 2019 |
| Contact name |
Hervé Seitz |
| Phone |
(508)856 1220
|
| Fax |
(508)856 2003
|
| URL |
http://www.umassmed.edu/bmp/faculty/zamore.cfm?start=0&
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Biochemistry and Molecular Pharmacology
|
| Lab |
870 P, Lazare Research Building
|
| Street address |
364 Plantation Street
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605-2324 |
| Country |
USA |
| |
|
| Platform ID |
GPL6664 |
| Series (1) |
| GSE11019 |
Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells |
|
| Relations |
| SRA |
SRX000323 |
