|
| Status |
Public on Jul 20, 2022 |
| Title |
Microdissected Rat Renal CCD, UUO_4_3Hr, RNA-Seq, Transcriptome 01 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
tissue: Kidney
group: UUO
|
| Treatment protocol |
For the unilateral ureteral obstruction (UUO) group, rats were anesthetized and the left ureter was exposed and separated through a flank incision. The left ureter was ligated with 4-0 silk at near the renal pelvis. For the sham control group, surgical procedures were the same as for UUO animals except that the ureter was not ligated.
|
| Growth protocol |
Pathogen-free male Sprague-Dawley rats weighing 120-160 g had free access to ad libitum drinking water and normal rodent chow before experiment. The rats were housed one per cage, maintained on a 12:12-h light-dark cycle, and acclimated to the housing conditions for 2 days before the experimental procedures.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For bulk kidney, obstructed kidneys from animals were rapidly removed and be processed individually by homogenizing in Trizol, then transferred to a 2.0 mL microcentrifuge tube for RNA extraction and library construction (TruSeq Stranded mRNA Library Prep Kit, Illumina) according to the manufacturer’s protocol. For microdissecting cortical collecting duct and cortical TAL, total RNA were extracted using the Direct-zol™ RNA Kits (Zymo Research) and cDNA was synthesized by SMARTer V4 Ultra Low RNA kit (Clontech). The cDNA was then amplified for 15 PCR cycles, purified by AmPure XP magnetic beads (Beckman Coulter Genomics), and eluted with 15 μL Elution Buffer. The purified cDNA was further quantified by Qubit. Library size distribution was determined using the Agilent 2100 bioanalyzer using High-Sensitive DNA kit. The Nextera XT DNA Library Preparation Kits (Illumina) was used to generate the libraries with input of 1 ng.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
UUO3H_RNAseq_TPM
|
| Data processing |
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.7.3
Transcript abundances in TPM were caculated by RSEM/1.3.3
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text files include TPM for each sample
|
| |
|
| Submission date |
May 11, 2021 |
| Last update date |
Jul 20, 2022 |
| Contact name |
Chih-Chien Sung |
| E-mail(s) |
[email protected]
|
| Phone |
886-2-87927213
|
| Organization name |
Tri-Service General Hospital, National Defense Medical Center
|
| Department |
Department of Medicine
|
| Street address |
No 325, Section 2, Cheng-Kung Road,Neihu
|
| City |
Taipei |
| State/province |
Taipei |
| ZIP/Postal code |
114 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL25029 |
| Series (1) |
| GSE174289 |
Early molecular events mediating loss of aquaporin-2 in kidney collecting duct during ureteral obstruction |
|
| Relations |
| BioSample |
SAMN19110535 |
| SRA |
SRX10863269 |
