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Sample GSM1553560

Query DataSets for GSM1553560

Status

Public on Feb 09, 2017

Title

NVS3

Sample type

SRA

Source name

Antennae

Organism

Apis mellifera

Characteristics

phenotype: non-VSH
mean age: 12.25
tissue: 4 pairs of antennae

Extracted molecule

total RNA

Extraction protocol

Bees were collected and flash frozen in liquid nitrogen, antennae were cut-off and RNA was isolated using Trizol reagent and following the Purelink Micro kit (Invitrogen) instructions.
RNA-Seq libraries were prepared with the 'TruSeq Stranded RNA sample preparation Kit' (Illumina) according to the manufacturer's instructions.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 2500

Description

Pseudo_Counts_VSH-NVS_RLE_RNA-Seq_Alaux.xls

Data processing

Image analyses and basecalling were performed using the HiSeq Control Software (HCS 2.2.38) and Real-Time Analysis component (RTA 1.18.61).
Demultiplexing was performed using Illumina's sequencing analysis software (CASAVA 1.8.2). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequence Analysis Viewer).
A splice junction mapper, TopHat2 (with bowtie 2.2.3), was used to align RNA-seq reads to Apis mellifera genome (Amel 4.5 NCBI) with a set of gene model annotations (ref_Amel_4.5_top_level.gff3 downloaded from NCBI on June 18, 2014). Final read alignments having more than 3 mismatches are discarded.
Counting was performed with HTSeq-count 0.6.1p1 (union mode). The data is from a strand-specific assay, the read has to be mapped to the opposite strand of the gene.
Differentially expressed genes were identified using the Bioconductor package edgeR (v3.4.0). Genes with less than 15 reads (cumulating all the analysed samples) for NUR and FOR conditions, and 20 reads for VSH and NVS conditions, were filtered and thus removed from the analysis. Data were normalized using Relative Log Expression (RLE) normalization factors. Genes with adjusted p-value less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: Amel_4.5 [Apis mellifera 4.5 (NCBI)]
Supplementary_files_format_and_content: Excel files with 3 columns for gene identification : the first one is the NCBI Gene ID (mandatory), the second one is the gene symbol (if any), and the third one is the BeeBase ID (if any). The next columns correspond to the normalized abundance measurements (RLE normalization using edgeR statistical package) for each sample.

Submission date

Nov 25, 2014

Last update date

May 15, 2019

Contact name

Cedric Alaux

E-mail(s)

cedric.alaux@paca.inra.fr

Organization name

INRA

Street address

Domaine Saint Paul, Site Agroparc