|
| Status |
Public on Apr 04, 2019 |
| Title |
Microdissected Rat Renal cTAL, Lithium_72h, RNA-Seq, Transcriptome 08 |
| Sample type |
SRA |
| |
|
| Source name |
cTAL_Li_72h
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
gender: male
tissue: Kidney
tissue sample: Microdissected Renal cTAL
agent: Lithium
time: 72h
|
| Treatment protocol |
Rats are exposed to food without (Control) or with 40mM lithium chloride (LiCl) /kg food for 0, 12, 24, 36, and 72 hrs
|
| 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 |
After microdissecting cortical collecting duct and cortical collecting duct, 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 |
Illumina HiSeq 3000 |
| |
|
| Description |
cTAL_Li_72h_8
|
| Data processing |
Sequenced reads were mapped to Ensembl rat gene set (Rnor_6.0) using STAR v2.5.2b
Transcript abundances in TPM were caculated by RSEM/1.2.31
Genome_build: Rnor_6.0 (Ensembl)
Supplementary_files_format_and_content: tab-delimited text file includes TPM for each sample
|
| |
|
| Submission date |
Jul 07, 2018 |
| Last update date |
Apr 04, 2019 |
| Contact name |
Lihe Chen |
| E-mail(s) |
lihe.chen@nih.gov
|
| Phone |
3015947152
|
| Organization name |
NHLBI
|
| Street address |
10 center drive MSC 1603, Building 10, Room 6N318
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL23945 |
| Series (1) |
| GSE116760 |
RNA-Seq and protein mass spectrometry in microdissected kidney tubules reveal signaling processes initiating lithium-induced nephrogenic diabetes insipidus |
|
| Relations |
| BioSample |
SAMN09628673 |
| SRA |
SRX4365113 |
