|
| Status |
Public on Oct 01, 2018 |
| Title |
983-LW-8 |
| Sample type |
SRA |
| |
|
| Source name |
WT_retina
|
| Organism |
Mus musculus |
| Characteristics |
strain background: C57BL/6
genotype/variation: wild type
age: 3 months old
treatment: naïve
tissue: retina
|
| Treatment protocol |
Naïve mice aged 3 months with no additional treatment.
|
| Growth protocol |
Tissue extracted from animals.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
983-LW-8-TAATGCGC-TATAGCCT_S392
|
| Data processing |
DNase-treated total RNA quality was assessed using the 2100 Bioanalyzer (Agilent). Samples with a RNA integrity number greater than 6 were used to generate polyA (mRNA) enriched libraries using stranded mRNA sample kits with indexed adaptors (New England BioLabs).
Library quality was assessed using the 2100 Bioanalyzer (Agilent) and libraries were quantitated using KAPA Library Quantification Kits (KAPA Biosystems).
Pooled libraries were subjected to 100 bp paired-end sequencing according to the manufacturer’s protocol (Illumina NovaSeq6000).
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files.
Reads were aligned to the GENCODE GRCm38.p5 genome using STAR v2.5.3a.
GENCODE vM12 gene annotations were provided to STAR to improve the accuracy of mapping. Quality control on raw reads was performed using FastQC.
featureCounts v1.15.2 was used to count the number of mapped reads to each gene.
Significantly differential expressed genes with adjusted p-value < 0.05 and absolute fold change > 2 were detected by DESeq2 v1.14.
Genome_build: GENCODE GRCm38.p5
Supplementary_files_format_and_content: counts
|
| |
|
| Submission date |
Jul 11, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
Lauren Katie Wareham |
| E-mail(s) |
[email protected]
|
| Phone |
8575408019
|
| Organization name |
Vanderbilt University Medical Center
|
| Department |
Vanderbilt Eye Institute
|
| Lab |
Sappington Lab
|
| Street address |
2213 Garland Avenue, MRBIV 11435a
|
| City |
Nashville |
| State/province |
Tennessee |
| ZIP/Postal code |
37232 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE116916 |
RNAseq quantitative analysis of naïve wild type and interleukin-6 knockout mice |
|
| Relations |
| BioSample |
SAMN09642192 |
| SRA |
SRX4378904 |
