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Sample GSM4282385 Query DataSets for GSM4282385
Status Public on Jan 28, 2020
Title NE1
Sample type SRA
Source name Retinal endothelial cells
Organism Mus musculus
Characteristics disease state: Naive
strain: C57BL/6
tissue: Retina
cell type: Retinal endothelial cells
Extracted molecule total RNA
Extraction protocol RNA extraction was performed using the MiRNeasy MicroKit (Qiagen) according to the manufacturer’s recommendations and a DNase step to avoid DNA contamination.
Indexed cDNA libraries were prepared using the Ovation SoLo RNAseq system (Nugen).
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
Description Naive retinal endothelial cells pool 1
Data processing The multiplexed libraries were loaded, and sequences were produced using a TruSeq PE cluster and SBS-kit on a HiSeq 1500 (Illumina).
Approximately 25 million paired-end reads/sample were mapped against the mouse reference genome (NCBI Build 37/ UCSC mm9) using STAR software to generate read alignments for each sample.
Expression levels were quantified using the featureCounts(9) tool and the UCSC RefSeq gene annotation as a reference (exons only, genes as meta features).
Differential analysis between groups was performed using the EdgeR package (quasi-likelihood F-tests). Normalized expression levels were estimated using the EdgeR rpm function and converted to log2 FPKM (fragments per kilobase of exon per million mapped reads) after resetting low FPKMs to 1.
Genome_build: NCBI Build 37/ UCSC mm9
Supplementary_files_format_and_content: Excel file include CPM values (Log2) for each sample
Submission date Jan 23, 2020
Last update date Feb 01, 2020
Contact name Frederick Libert
Organization name ULB
Department IRIBHM
Lab C2-140
Street address 808 route de Lennik
City Brussels
ZIP/Postal code B-1070
Country Belgium
Platform ID GPL18480
Series (1)
GSE144168 Retinal endothelial cell phenotypic modifications during experimental autoimmune uveitis: a transcriptomic approach
BioSample SAMN13910628
SRA SRX7625925

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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