|
| Status |
Public on Nov 02, 2012 |
| Title |
miRNA-seq_CS_ZT0 |
| Sample type |
SRA |
| |
|
| Source name |
Drosophila head
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Canton S
age: adult
tissue: head
circadian time point: ZT0
molecule subtype: Small RNAs 18-20 nucleotides in length, 2s rRNA depleted
|
| Treatment protocol |
Flies were collected at specified time point and frozen on dry ice, heads were removed.
|
| Growth protocol |
Adult flies were kept in constant 12 hr:12 hr light:dark conditions for 3 days before collection
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol reagent (Invitrogen) as suggested by the supplier. Small RNA sequencing libraries were essentially prepared as described in (Seitz et al., 2008) with one exception: The 2S rRNA was depleted by hybridizing to a DNA oligonucleotide followed by RNaseH treatment. Following depletion of 2S rRNA, 19 to 29 nucleotide long RNAs were gel purified and adapters were ligated at 3’ and 5’ end using Rnl2 [(1-249) Ho et al., 2004] and T4 RNA ligase (Ambion) respectively. RNA was PCR amplified using primers corresponding to the adapters and the PCR products were gel purified on a 2% agarose gel.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
The first 20 bases of fasta formatted reads were mapped to the Drosophila melanogaster genome (dm3) with SeqMap (Jiang et al 2008) using the following command allowing up to two mismatches in the alignment: seqmap-1.0.12-linux-64 2 sequence.fa Dm_all_seqs.fa sequence.seqmap.out /match_shorter_probes /cut:1,20
Reads mapping to miRNA genomic locations were scanned for the presence of the entire mature miRNA sequence. Drosophila miRNA genomic locations were downloaded from www.mirbase.org. Read counts were normalized to the total number of mapped reads per sample. Cycling miRNAs were identified as described (Wijnen et al 2005).
wig files were generated using custom-written perl scripts for purpose of visualization.
Genome_build: dm3
Supplementary_files_format_and_content: wig files generated using custom-written perl scripts are provided for visualization on Genome Browsers.
|
| |
|
| Submission date |
Sep 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Pescatore |
| E-mail(s) |
[email protected]
|
| Phone |
781-736-3161
|
| Fax |
781-736-3164
|
| Organization name |
Brandeis University / HHMI
|
| Department |
Biology
|
| Lab |
Michael Rosbash
|
| Street address |
415 South Street
|
| City |
Waltham |
| State/province |
MA |
| ZIP/Postal code |
02454 |
| Country |
USA |
| |
|
| Platform ID |
GPL9061 |
| Series (2) |
| GSE40943 |
The Oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs [miRNA-seq]. |
| GSE40981 |
The Oscillating miRNA 959-964 cluster impacts Drosophila feeding time and other circadian outputs. |
|
| Relations |
| SRA |
SRX187558 |
| BioSample |
SAMN01178449 |
