|
| Status |
Public on May 01, 2018 |
| Title |
AdrGland KO F 2062 |
| Sample type |
SRA |
| |
|
| Source name |
adrenal gland tissue
|
| Organism |
Mus musculus |
| Characteristics |
strain: 129SVEV
gender: Female
genotype: Siah1a -/-
tissue: adrenal gland
agent: none
|
| Treatment protocol |
mice were injected IP with 100ug/kg of ACTH for 1 hour
|
| Growth protocol |
adrenal glands were harvested from mice not treated or injected IP with 100ug/kg of ACTH for 1 hour
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from adrenal glands using TRIzol (Ambion) and digested with DNase I. cDNA was synthesized using oligo-dT and random hexamer primers
barcoded libraries were made using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB). Libraries were pooled and single-end sequenced (1X75) on an Illumina NextSeq 500 using the High Output V2 kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Illumina’s Basespace was used to convert bcl files to FASTQ files and de-multiplex the samples
Sequenced reads were assessed with FastQC v0.11, then mapped to mm10 whole genome using TopHat2 v2.0.13 and Bowtie2 v2.2.5.0 with --b2-sensitive option and default parameters
Partek Genomics Suite v6.6 was applied for quantification based on RefSeq transcript model (2016-02-02)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include raw read count and RPKM values for each sample
|
| |
|
| Submission date |
Aug 23, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jian-Liang Li |
| Organization name |
NIEHS
|
| Street address |
111 TW Alexander Dr
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE102963 |
The E3 ubiquitin ligase Siah1 regulates adrenal gland organization and hyperaldosteronism |
|
| Relations |
| BioSample |
SAMN07542370 |
| SRA |
SRX3115974 |
