|
| Status |
Public on Nov 28, 2012 |
| Title |
RIPseq_sz-Venus_IP |
| Sample type |
SRA |
| |
|
| Source name |
sz-Venus expressed
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: w1
tissue: ovary
rip antibody: UAP-Venus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
UAP56-Venus and sz-Venus were immunoprecipated by ANTI-FLAG® M2 Affinity Gel (Sigma A2220) and eluted with 200μg/ml FLAG® Peptide (Sigma F3290). Three biological replicates were performed for each IP. Total RNA was extracted from the input lysate and the beads using RNeasy Micro Kit (Qiagen) using the manufacturer’s protocol. Strand-specific RNA sequencing was performed after depletion of ribosomal RNAs using Ribo-Zero (Epicenter Inc) by a modification of the procedure of Parkhomchuk et al. (Parkhomchuk et al., 2009), described in detail elsewhere (Z. Zhang and P. D. Zamore, manuscript in preparation).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RNA immunoprecipitation (RIP)
|
| Data processing |
Library strategy: RIP-Seq
Base calling and demultiplexing was performed using CASAVA 1.8
Alignments were performed using TopHat version 2.0.4
bedGraph files were generated from bam files from Tophat, and were normalized by the sequencing depth and the number of times the reads are mapped to the genome.
Genome_build: dm3
Supplementary_files_format_and_content: bedGraph files were generated from bam files from Tophat, and were normalized by the sequencing depth and the number of times the reads are mapped to the genome.
|
| |
|
| Submission date |
Oct 02, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Jie Wang |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Massachusetts Medical School
|
| Department |
Program in Bioinformatics and Integrative Biology
|
| Lab |
Zhiping Weng
|
| Street address |
364 Plantation St.
|
| City |
Worcester |
| State/province |
MA |
| ZIP/Postal code |
01605 |
| Country |
USA |
| |
|
| Platform ID |
GPL13304 |
| Series (2) |
| GSE35637 |
UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery [RNA-Seq and RIP-Seq] |
| GSE35638 |
UAP56 couples piRNA clusters to the perinuclear transposon silencing machinery |
|
| Relations |
| SRA |
SRX190814 |
| BioSample |
SAMN01737675 |
