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Sample GSM1386713 Query DataSets for GSM1386713
Status Public on May 15, 2016
Title Larval CNS
Sample type SRA
Source name Larval ventral ganglion w/optic lobes
Organism Drosophila melanogaster
Characteristics genotype/variation: w[1118] Iso31
tissue: brain (ventral ganglion w/optic lobes)
developmental stage: larvae
age: third instar
Growth protocol Flies were grown on standard Bloomington media at 24 C in a humidified diurnal incubator (BioCold). For larval CNS collection, flies were grown in vials initially containing 15 females and 5 males (P0). Ventral ganlia (including the optic lobes but not the eye imaginal discs) were explanted from wandering third instar larvae (F1). For adult brain collection, remaining larvae in these vials were allowed to pupate and brains explanted from adults collected 3-5 days post-eclosion (F1). In both cases, the male:female ratio was approximately 50:50.
Extracted molecule total RNA
Extraction protocol For each sample, tissues were explanted from ~100 animals by microdissiction and immediately transferred to ice-cold Trizol reagent (Life Technologies). Total RNA was extracted using Trizol reagent and standard protocols.
Illumina TruSeq Small RNA Sample Prep Kit (Cat#RS-200-0012) was used with 1 ug of total RNA for the construction of both sequencing libraries. Indexes RPI4 and RPI5 were added to adult and larval small RNAs (respectively) for multiplex sequencing. Small RNA libraries were prepared using standard Illumina protocols.
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 2000
Data processing Illumina Casava v1.8 software was used for basecalling and de-multiplexing.
For identifying known miRNAs, sequence reads were trimmed for adapter sequences and mapped to known Drosophila miRNAs (miRBase v20) using the CLC Genomics Workbench v7.0 small RNA workflow. Parameters used were: miR length = 18-27; min reads = 1.
For identifying novel miRNAs, sequence reads were trimmed for adapter sequences and mapped to the Drosophila genome (UCSC assembly dm3) using miRDeep* (An et al. Nucleic Acids Research 2013). Parameters used were: miR length = 18 to 23; min phred = 20; max multimap = 101; min reads = 5; min score = -10.
Anaylsis of differential known miRNA expression including statisitical analysis was done using normlized miRNA counts (in RPM) in CLC Genomics Workbench v7.0. Kal's test (Kal et al. Mol Biol Cell 1999) was used to calculate Bonferroni corrected p-values.
Genome_build: miRBase v20; Release 5
Supplementary_files_format_and_content: Excel spreadsheets including miRNA abundance measurements (normalized to RPM), novel miRNAs, and analysis of differential miRNA expression with statistics.
Submission date May 15, 2014
Last update date May 15, 2019
Contact name Scott A Barbee
Phone 303-871-3582
Organization name University of Denver
Department Biological Sciences
Street address 2190 E. ILIFF Ave.
City Denver
State/province CO
ZIP/Postal code 80208
Country USA
Platform ID GPL13304
Series (1)
GSE57687 Profling of the Drosophila melanogaster neuronal microRNA transcriptome by small RNA deep sequencing
BioSample SAMN02777981
SRA SRX542994

Supplementary file Size Download File type/resource
GSM1386713_larvalCNS_novel.xlsx.gz 51.8 Kb (ftp)(http) XLSX
GSM1386713_larvalCNS_trimmed_small_RNA.xlsx.gz 15.1 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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