|
| Status |
Public on May 22, 2019 |
| Title |
RT - RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
trunk tissue
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Raldh2 (Aldh1a2) knockout
developmental stage: stage E8.5 embryo
tissue: dissected embryonic trunk tissue
|
| Growth protocol |
Mice were maintained on normal chow.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara).
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA). Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Wt_vs_Rt.gene_exp.diff.xlsx
|
| Data processing |
Read data was processed in BaseSpace (basespace.illumina.com).
Reads were aligned to to Mus musculus genome (mm10) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Differential transcript expression was determined using the Cufflinks Cuffdiff package (https://github.com/cole-trapnell-lab/cufflinks).
Genome_build: Mus musculus genome mm10
Supplementary_files_format_and_content: Read FPKM and Log2 fold differential expression, and FDR corrected Q-values
|
| |
|
| Submission date |
May 21, 2019 |
| Last update date |
May 23, 2019 |
| Contact name |
Brian Patrick James |
| E-mail(s) |
[email protected]
|
| Organization name |
Sanford Burnham Prebys Medical Discovery Institute
|
| Department |
Genomics
|
| Lab |
James
|
| Street address |
10901 North Torrey Pines Road
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE131584 |
Global identification of retinoic acid regulated genes |
|
| Relations |
| BioSample |
SAMN11808383 |
| SRA |
SRX5878156 |
