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Sample GSM2679434

Query DataSets for GSM2679434

Status

Public on Jun 20, 2018

Title

VSMC_DN4

Sample type

SRA

Source name

Brain cortex

Organism

Rattus norvegicus

Characteristics

strain: Sprague-Dawley
developmental stage: 4-5 weeks
gender: male
tissue: Brain
cell type: VSMC

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using the RNeasy® Micro Kit (Qiagen). Messenger (polyA+) RNAs were purified from 100 ng of total RNA using oligo(dT). All samples had RNA integrity numbers ranging from 6.40 to 8.50 as assessed by Agilent Bioanalyzer.
Libraries were prepared using the strand specific RNA-Seq library preparation TruSeq Stranded mRNA kit (Illumina)

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

Before mapping, poly N read tails were trimmed, reads ≤40 bases were removed, and reads with quality mean ≤30 were discarded.
Transcript abundances (in Transcripts Per Million, TPM) and counts (in number of reads) were estimated using Salmon 0.8.0 (Patro R et al. Nat. Methods. 2017;14:417–419. )
Reads were aligned against the rat transcriptome using Rattus_norvegicus.Rnor_6.0.cdna.all.fa.gz Ensembl annotation file (ftp://ftp.ensembl.org/pub/release-87/fasta/rattus_norvegicus/cdna/).
Transcript-level estimates were summed within genes to obtain TPM and counts estimates at the gene level using the Tximport package (Soneson C et al. F1000Res. 2015;4:1521.).
The whole dataset contains 14607 genes with at least one read in each sample (after summation over technical replicates)
Differential gene expression was estimated using DESeq2 and was expressed as Log2FC, defined as the Log2 of the Fold Change between mean normalized counts in PC vs VSMC
Genome_build: Rnor_6.0 (Ensembl release 87)
Supplementary_files_format_and_content: File including Ensembl_Gene_ID, Entrez_Gene_ID, Gene_Symbol, Gene_Description, MeanTPM_VSMC, MeanTPM_mcPC, MeanCounts_VSMC, MeanCounts_mcPC, MeanLength_VSMC, MeanLength_mcPC, MeanCountsNorm_VSMC, MeanCountsNorm_mcPC, baseMean, log2FoldChange, lfcSE, lfc pvalue, lfc padj

Submission date

Jun 22, 2017

Last update date

May 15, 2019

Contact name

bruno saubamea

E-mail(s)

[email protected]

Organization name

Université Paris Descartes

Department

Faculté de Pharmacie de Paris