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| Status |
Public on Jun 20, 2018 |
| Title |
mcPC_DK2 |
| Sample type |
SRA |
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| Source name |
Brain cortex
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
developmental stage: 4-5 weeks
gender: male
tissue: Brain
cell type: PC
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| 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)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| 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
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| Submission date |
Jun 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
bruno saubamea |
| E-mail(s) |
bruno.saubamea@parisdescartes.fr
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| Organization name |
Université Paris Descartes
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| Department |
Faculté de Pharmacie de Paris
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| Lab |
INSERM UMR-S1144
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| Street address |
4 avenue de l'observatoire
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| City |
paris |
| ZIP/Postal code |
75006 |
| Country |
France |
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| Platform ID |
GPL20084 |
| Series (1) |
| GSE100355 |
Isolation and differential transcriptome of vascular smooth muscle cells and mid-capillary pericytes from the rat brain |
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| Relations |
| BioSample |
SAMN07268984 |
| SRA |
SRX2946670 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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