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Sample GSM2363305

Query DataSets for GSM2363305

Status

Public on Nov 30, 2016

Title

ovoD1 smRNA

Sample type

SRA

Source name

fat body, ovoD1

Organism

Drosophila melanogaster

Characteristics

genotype/variation: ovoD1
tissue: fat body
Sex: female
age: 10d

Treatment protocol

Relevant body parts dissected from 25-100 flies. For fat bodies, abdominal cavity was cut open and fat tissue scraped from inside of body wall after discarding ovaries and gut.

Growth protocol

Female flies grown on 15% dextrose, 15% yeast, 2% agar food for 10days post eclosion, passed to new food vials every 2-3 days.

Extracted molecule

total RNA

Extraction protocol

Total RNA was isolated using the protocol from the mirVana kit (Ambion).
RNA-seq: 100ng total RNA used as input for Nugen Universal RNA-seq kit, prepped as per manufacturer's instructions using Drosophila rRNA depletion module.
Small RNA-seq: 1ug of total RNA was oxidized with 200mM sodium periodate per Zamore lab protocol (http://www.umassmed.edu/zamore/resources/protocols/), purified with Zymo RNA Minelute cleanup kit, then used as input for NEBNext Multiplex Small RNA Library Prep kit (NEB catalog #7300S) per manufacturer's instructions.

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina HiSeq 2500

Description

Small RNA-seq

Data processing

Basecalling performed with Illumina CASAVA 1.8.
Adapter sequences trimmed using cutadapt.
RNA-seq reads aligning to rRNA were removed using bowtie2 alignment to known dm3 rRNA sequences.
RNA-seq reads aligned to dm3 genome using Tophat 2.0.10.
Small RNA-seq reads aligned to dm3 genome using bowtie1 -v 1.
Count tables and RPKM values performed using easyRNASeq Bioconductor package, with geneModels summarization parameter. Normalized easyRNASeq RPKM values are reported in head.thorax.abdomen.ovary.easyRNAseq.rpkm.txt.
Transposable element quantification performed using RepEnrich software (Criscione et al., BMC Genomics 15:583), using RepBase transposable element annotation.
RNA-seq transposable element normalization, log2 fold change calculation, and differential expression testing was performed using edgeR package, with correction for batch effects as described in edgeR vignette. Normalized counts and log2 Fold Changes are reported in piwi.rnaseq.repenrich.edgeR.txt.
Small RNA-seq transposable element counts were normalized to reads mapping to cisNATs and structured loci, described in Malone et al., Cell 137:522-35. Normalized read counts and log2 fold changes are reported in piwi.pirna.repenrich.antisense.normalized.log2FC.txt.
Rawcounts txt files contain raw read counts output from easyRNASeq or RepEnrich as appropriate.
Genome_build: dm3 (Release 5)
Supplementary_files_format_and_content: *txt: Tab-delimited text files include Count/RPKM tables.

Submission date

Oct 27, 2016

Last update date

May 15, 2019

Contact name

Jason G Wood

E-mail(s)

[email protected]

Organization name

Brown University

Department

MCB