|
| Status |
Public on Jan 28, 2020 |
| Title |
DR2 |
| Sample type |
SRA |
| |
|
| Source name |
Total retinal cells
|
| Organism |
Mus musculus |
| Characteristics |
disease state: Experimental autoimmune uveitis
strain: C57BL/6
tissue: Retina
cell type: Total retinal 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 |
EAU retinal cells pool 2
|
| 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 |
| E-mail(s) |
flibert@ulb.ac.be
|
| 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 |
|
| Relations |
| BioSample |
SAMN13910632 |
| SRA |
SRX7625921 |
