|
| Status |
Public on Jan 01, 2014 |
| Title |
Drosophila_wild-type 3d_head_no-oxidation |
| Sample type |
SRA |
| |
|
| Source name |
wild-type male flies
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: 3d
gender: male
tissue: head
genotype: 5905
treatment of total rna prep: without oxidation/β-elimination
|
| Treatment protocol |
Whole male flies were collected and aged to 3d and 30d.
|
| Growth protocol |
Flies were raised at 25˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Heads were collected on dry ice, followed by RNA preparation and oxidation/β-elimination.
Libraries were prepared according to Illumina's TruSeq small RNA sample preparation kit (#RS-200-0012, Illumina, Inc. San Diego, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
3d wild-type small RNAs without oxidation/β-elimination
MA6/5905 3d head no-oxidation
|
| Data processing |
For base-calling Illumina Casava version 1.8.2 was used
Sequenced reads were trimmed for adapter sequence, then mapped to dm3 genome assembly for drosophila melanogaster using the RUM v1.11 pipeline by setting Bowtie to allow 0 mismatches and Blat to require 100% sequence identity
The uniquely mapping sequences with length between 16-35 nt were checked for overlap with the miRNAs
Genome_build: dm3
Supplementary_files_format_and_content: Tab-delimited files containing the read counts corresponding to each uniquely mapping sequence with length between 16-35 nt
|
| |
|
| Submission date |
Dec 04, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Ammar S Naqvi |
| E-mail(s) |
[email protected]
|
| Phone |
6318755794
|
| Organization name |
Childrens Hospital of Philadelphia
|
| Department |
Center for Data-Driven Discovery in Biomedicine
|
| Lab |
Grigoriev Lab
|
| Street address |
2716 South Street
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19146 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE52960 |
small RNA deep-sequencing with oxidation/β-elimination with age in Drosophila |
| GSE52963 |
Impact Of Age-Associated Increase In 2'-O-Methylation Of miRNAs On Aging And Neurodegeneration In Drosophila |
|
| Relations |
| BioSample |
SAMN02434678 |
| SRA |
SRX386669 |
