|
| Status |
Public on Oct 31, 2009 |
| Title |
2´-O-methylated small RNAs from dcr-2 homozygous flies |
| Sample type |
SRA |
| |
|
| Source name |
fly heads
|
| Organism |
Drosophila melanogaster |
| Characteristics |
genotype: dcr-2^L811fsX mutant strain (described in Lee et al., 2004, Cell 117:69)
tissue: head
|
| Treatment protocol |
Heads were dissected by vigorous shaking in liquid nitrogen in a metal sieve, as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)). Total RNA was extracted using the mirVana kit (Ambion), then short (18-29 nt) RNAs were gel-purified. 2S rRNA was depleted as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)). When applicable: small RNA preparations were oxidized with periodate in the presence of boric acid as described in Horwich et al. (2007) Curr. Biol. 17(14):1265-1272, except the final (alkaline) step was omitted.
|
| Growth protocol |
Flies were grown according to standard protocols.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
3´ adapter (described in Lau et al., 2001, Science 294:858) and 5´ adapter (sequence: 5´dAdTdC dGdTrA rGrGrC rArCrC rUrGrA rArA3´) were ligated to the small RNAs, then the library was reverse-transcribed and amplified as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
oxidized with periodate in presence of boric acid before library preparation
|
| Data processing |
For each sequence read, the first occurrence of the 6-mer perfectly matching the 5′ end of the 3′ linker was identified. Sequences without a match were discarded. Sequences that mapped to let-7 without connonical 5'end have been removed because of contamination
|
| |
|
| Submission date |
Oct 29, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Jia Xu |
| E-mail(s) |
Jia.Xu@umassmed.edu
|
| Organization name |
UMASSMED
|
| Department |
Program in Bioinformatics and Integrative Biology
|
| Lab |
Weng
|
| Street address |
55 Lake Avenue North
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01655 |
| Country |
USA |
| |
|
| Platform ID |
GPL9058 |
| Series (1) |
| GSE18806 |
Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway |
|
| Relations |
| Reanalyzed by |
GSM3274545 |
| SRA |
SRX014452 |
| BioSample |
SAMN00006266 |
