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Sample GSM2402717

Query DataSets for GSM2402717

Status

Public on Feb 15, 2017

Title

Repo/TDP43:S23_small RNA

Sample type

SRA

Source name

Head

Organism

Drosophila melanogaster

Characteristics

strain: 2U
tissue: head
genotype/variation: Repo/TDP43

Extracted molecule

total RNA

Extraction protocol

All small RNA libraries were constructed from 15-20 ug of TRIzol isolated total RNA.
18-29 nucleotide long small RNAs were size selected on 15% PAGE-UREA gel. After 3’- and 5’-adapter ligation, subsequent gel purification steps and reverse transcription cDNAs were PCR amplified with barcoded primers. PCR products were size selected on 6% PAGE gel, and quantified on Bioanalyzer. Loading concentrations were determined using the NEBNext Library Quant kit for Illumina (NEB). The libraries were sequenced on illumina NextSeq 500 platform.

Library strategy

ncRNA-Seq

Library source

transcriptomic

Library selection

size fractionation

Instrument model

Illumina NextSeq 500

Description

processed data file: small_RNA_count.txt

Data processing

Reads were mapped to the Drosophila dm3 genome with Bowtie allowing up to 2 mismatches and a maximum of 100 multiple alignments.
Feature abundances were obtained by annotating reads based on genomic locations against ribosomal RNAs, microRNAs (miRBase), exons (RefSeq), transposable elements (FlyBase), introns (RefSeq), and piRNA clusters (proTRAC) using intersectBed from BedTools.
For the multiple mapped reads, the read counts were evenly distributed between all equivalently aligned matches.
Genome_build: dm3
Supplementary_files_format_and_content: raw counts of sequencing reads for the genomic features

Submission date

Nov 23, 2016

Last update date

May 15, 2019

Contact name

Wen-Wei Liao

Organization name

Cold Spring Harbor Laboratory

Street address

1 Bungtown Road

City

Cold Spring Harbor