|
| Status |
Public on Feb 09, 2017 |
| Title |
RAG1-/-Sgo1-/+ (L6) |
| Sample type |
SRA |
| |
|
| Source name |
RAG1-/-Sgo1-/+, lung
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: RAG1-/-Sgo1-/+
tissue: normal-looking lung
|
| Treatment protocol |
No experimental treatment was applied
|
| Growth protocol |
all mice were maintained to 12 months of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from normal-looking lung tissues using Trizol reagent.
Libraries were prepared according to Illumina's instructions accompanying the RNA TruSeq V2 Library construction kit. Libraries were sequenced on the Illumina MiSeq following the manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina MiSeq |
| |
|
| Description |
L6
|
| Data processing |
Genesifter software was used for base-calling and alignment.
BWA Paired-End (GATKv3) pipeline was used to align with Mus musculus (build 37.2) genome. Pairwise and Cluster analyses were done using Genesifter software and differential gene lists were exported as tab delimited files.
Pairwise settings were as follows: normalize to mapped reads, statistical analysis using EdgeR differential genes narrowed to 2 fold min for final analysis, data correct using Benjamini Hochberg method.
Pairwise analysis was done using RPKMs and determination of fold significance using EdgeR with a significance value (p value) cutoff of 0.05. Then fold cutoff was set to 2.0-fold for identifying differentially expressed genes and for subsequent pathway analysis.
Genome_build: Mus musculus build 37.2 (MGSCv37)
Supplementary_files_format_and_content: [.txt] RPKMs and differentially expressed genes
|
| |
|
| Submission date |
Jul 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Hiroshi Y Yamada |
| Organization name |
OUHSC
|
| Department |
Medicine
|
| Street address |
975 NE 10th st. BRC1207
|
| City |
Oklahoma City |
| State/province |
Oklahoma |
| ZIP/Postal code |
73104 |
| Country |
USA |
| |
|
| Platform ID |
GPL16417 |
| Series (1) |
| GSE84383 |
NGS-mRNA in lung tissues in RAG1-/- and in RAG1-/- Sgo1-/+ mice |
|
| Relations |
| BioSample |
SAMN05390880 |
| SRA |
SRX1948855 |
