|
| Status |
Public on Feb 13, 2019 |
| Title |
MCW SS 0.4% salt_RNA-seq Replicate 1 [859] |
| Sample type |
SRA |
| |
|
| Source name |
MCW SS 0.4% salt
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: MCW SS
diet: Low salt, 0.4% NaCl
tissue: renal outer medulla
|
| Treatment protocol |
HS_SCR rats were treated with intra-renal administration of a scrambled GapmeR (4 mg/kg) and fed the 4% NaCl diet for 7 days. HS_DT rats were treated with intra-renal administration of GapmeR’s targeting Dnmt3a and Tet3 (2 mg/kg each) and fed the 4% NaCl diet for 7. “0.4% salt” rats were surgically prepared in the same way as the groups of HS_SCR and HS_DT, but used for tissue collection just prior to when we would initiate the GapmeR treatment and high salt diet.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Renal outer medulla tissues were collected, and RNA were extracted from these tissues using using Trizol reagent.
Libraries for RNA-Seq were prepared using a NeoPrep System from Illumina, following the vendor's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Liang_LOM_859_GTGGCC_L008
|
| Data processing |
Data QC and trim with trim_galore version 0.2.5
Read alignment with TopHap version 2.1.1
Transcript quantification and normalization with cufflinks version 2.2.1
Differential expression analysis with cufflinks version 2.2.1
Genome_build: rn5
Supplementary_files_format_and_content: transcript/gene abundance
|
| |
|
| Submission date |
May 10, 2018 |
| Last update date |
Feb 13, 2019 |
| Contact name |
Pengyuan Liu |
| E-mail(s) |
pliu@mcw.edu
|
| Phone |
4149552833
|
| Organization name |
Medical College of Wisconsin
|
| Department |
Physiology
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
Wisconsin |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL14844 |
| Series (2) |
| GSE114334 |
DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension [RNA-seq] |
| GSE114335 |
DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension |
|
| Relations |
| BioSample |
SAMN09197017 |
| SRA |
SRX4071267 |
