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Sample GSM2099089

Query DataSets for GSM2099089

Status

Public on Mar 24, 2017

Title

low detergent rep 1

Sample type

SRA

Source name

Fly heads

Organism

Drosophila melanogaster

Characteristics

tissue: fly heads
treatment: low detergent

Extracted molecule

total RNA

Extraction protocol

For head1 and 2 samples we followed the original fly head homogenization protocol (Huang et al 2013 Pbio PMID: 24348200). For the Heads 3 and 4 sample 200 heads were frozen and lysed in 500ul of lysis buffer (30 mM HEPES KOH at pH 7.4, 100 mM KAcetate, 2 mM MgAcetate, 5% glycerol, 0.1% Triton X-100, 1 mM EGTA, 5 mM DTT, 0.4 U/μL murine RNase inhibitor [NEB], protease inhibitors (Complete mini, Roche), and 100ug/ml CHX). ribosome-protected RNA fragments were isolated using previously publish protocol (Calviello L et al 2015 nature methods PMID: 26657557)
RNA libraries were prepared using previously publish protocol (Calviello L et al 2015 nature methods PMID: 26657557)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Description

ribosome bound RNA

Data processing

Illumina adaptors were removed using cutadapt 1.9.1
Removing PCR duplications
Trimming four bases from both ends of the reads (these are UMIs)
Removing ribosoal RNA reads from the files
Alignment aginst circRNA dataset
Genome_build: dm3
Supplementary_files_format_and_content: Table with list of circRNA detected in the footprinting data

Submission date

Mar 25, 2016

Last update date

May 15, 2019

Contact name

Sebastian Kadener

E-mail(s)

[email protected]

Organization name

Brandeis University

Street address

415 South Street