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Sample GSM3309458

Query DataSets for GSM3309458

Status

Public on Oct 19, 2018

Title

LAFW

Sample type

SRA

Source name

Left atrial free wall

Organism

Oryctolagus cuniculus

Characteristics

tissue: heart
heart region: Left atrial free wall
breed: New Zealand White Rabbit

Extracted molecule

total RNA

Extraction protocol

Tissue samples were snap frozen in liquid nitrogen, RNA was extracted using Trizol and further purified using the Nucleospin RNA XS kit. For library preparation, 450 ng of RNA was used.
The Truseq Stranded Total RNA protocol was used for library preparation. Cytoplasmic and mitochondrial rRNA was depleted using Ribo-Zero Gold. 10 PCR cycles were performed to amplify the cDNA

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

The reads were trimmed with ILLUMINACLIP:./adapters_list_v6.fa:2:40:15 MINLEN:15
Using HISAT2 (v2.0.4), the reads were aligned to the genome.
Counts are obtained using HTSeq (v0.6.1)
Statistical analyses are performed using the edgeR (Robinson et al., 2010) and limma/voom (Ritchie et al., 2015) R packages.
All genes with no counts in any of the samples are removed whilst genes with more than 5 reads in at least 2 of the samples are kept.
Count data are transformed to log2-counts per million (logCPM), normalized by applying the trimmed mean of M-values method (Robinson et al., 2010) and precision weighted using voom.
Differential expression is assessed using an empirical Bayes moderated t-test within limma’s linear model framework including the precision weights estimated by voom. Resulting P values are corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Genes are re-annotated using biomaRt using the Ensembl genome databases (v91).
Genome_build: Genome and GTF were obtained from Ensembl (v0.89): OryCun2.0 (assembly GCA_000003625.1) and Oryctolagus_cuniculus.OryCun2.0.89.asFasta.gtf, respectively.
Supplementary_files_format_and_content: Excel file with counts

Submission date

Jul 27, 2018

Last update date

Oct 19, 2018

Contact name

Vincent M. Christoffels

E-mail(s)

v.m.christoffels@amsterdamumc.nl

Phone

0205667821

Organization name

Amsterdam UMC