|
| Status |
Public on Jan 01, 2014 |
| Title |
Drosophila_3d_whole fly_Ago1-IP |
| Sample type |
SRA |
| |
|
| Source name |
3d FLAG-HA-Ago2 male flies
|
| Organism |
Drosophila melanogaster |
| Characteristics |
age: 3d
gender: male
tissue: whole fly
genotype/variation: FLAG-HA-Ago2
rip antibody: anti-Ago1 (Abcam, ab5070)
|
| 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 |
Immunoprecipitation was performed with anti-Ago1 (ab5070) or anti-FLAG M2 beads (Sigma A2220), followed by purification of small RNA fraction.
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 Ago1-IP small RNAs from FLAG-HA-Ago2 flies
MA10/Ago1-IP 3d
|
| 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 Naqvi |
| E-mail(s) |
ammar.naqvi@rutgers.edu
|
| Phone |
631-875-5794
|
| Organization name |
Rutgers University
|
| Department |
Computational and Integrative Biology
|
| Lab |
Grigoriev Lab
|
| Street address |
303 COOPER STREET
|
| City |
Camden |
| State/province |
New Jersey |
| ZIP/Postal code |
08102 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE52961 |
Ago1 vs Ago2-IP small RNA deep-sequencing with age in Drosophila |
| GSE52963 |
Impact Of Age-Associated Increase In 2'-O-Methylation Of miRNAs On Aging And Neurodegeneration In Drosophila |
|
| Relations |
| BioSample |
SAMN02434681 |
| SRA |
SRX386673 |
