|
| Status |
Public on Feb 13, 2019 |
| Title |
MCW SS HS_DT, Replicate 4 [783] |
| Sample type |
SRA |
| |
|
| Source name |
MCW SS HS_DT
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: MCW SS
diet: high salt, 4.0%, NaCl
treatment: GapmeR's targetting Dnmt3 and Tet3
tissue: renal outer medulla
|
| Treatment protocol |
MCW SS LS rats were maintained on a purified diet, AIN-76A, containing 0.4% NaCl until 8 weeks old. CRL SS LS rats were maintained a non-purified diet, 5L2F, containing 0.75% NaCl until 8 weeks old. MCW SS HS and CRL SS HS rats were maintained on AIN-76A diet containing 4% NaCl for 14 days starting at 6 weeks of age. 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 |
genomic DNA |
| Extraction protocol |
Renal outer medulla tissues were collected, and genomic DNA was extracted using PureLink genomic DNA mini kit
Libraries for RRBS were prepared and sequenced largely following the protocols described by Gu, et al (Nat Protoc. 2011;6(4):468-81)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
Reduced Representation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
RRBS_LOM783_TTAGGC_L008
processed data file: RRBS.dataset2.processed.txt.gz
|
| Data processing |
Data QC and trim with trim_galore version 0.2.5
Read alignment with methylcoder version 2012-07-27
CpGs calling with methylcoder version 2012-07-27
Genome_build: rn5
Supplementary_files_format_and_content: read counts of methylated and unmethylated cyttosines at CpG sites
|
| |
|
| 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) |
| GSE114333 |
DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension [RRBS-seq] |
| GSE114335 |
DNA de novo (de)Methylation in the Kidney Contributes to Salt-Induced Hypertension |
|
| Relations |
| BioSample |
SAMN09197018 |
| SRA |
SRX4071262 |
