|
| Status |
Public on May 16, 2022 |
| Title |
mpkCCD cell-shGR1-Vehicle |
| Sample type |
SRA |
| |
|
| Source name |
mpkCCD cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: kidney collecting duct cell
cell passages: 18-32
treatment: Glucocorticoid receptor knockdown with small hairpin sequence 1 (shRNA TRCN0000238464)
|
| Treatment protocol |
To facilitate cell polarization, FBS and supplements, except dexamethasone, were removed from the medium in both control and glucocorticoid receptor knockdown cells under the vehicle conditions.
|
| Growth protocol |
The mpkCCD cells were grown on 12-well transwell in DMEM/Ham's F-12 medium containing 2% fetal bovine serum (FBS) and supplements.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After PBS washes, cells were lysed in Trizol reagent. Total RNA was extracted with the RNA extraction kit (Cat. E1011-A, ZYMO Research, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Vehicle condition (no vasopressin stimulation)
|
| Data processing |
Illumina bcl2fastq v2.20 program was used for basecalling.
Sequence reads were aligned to GRCm39 genome by HISAT2 program.
Differential expression analysis was performed using cuffdiff (cufflinks v2.2.1) with genome bias detection/correction and Welgene Biotech's in-house pipeline.
Genes with low expression level (< 0.3 FPKM value) were excluded.
Transcripts with log2 (control/glucocorticoid knockdown) values < -1 or > 1 were considered differentially expressed.
Genome_build: GRCm39
Supplementary_files_format_and_content: xlsx. Files included every gene's FPKM, FPKM ratio between shctrl and shGR, q-value and p-value.
|
| |
|
| Submission date |
Jan 20, 2022 |
| Last update date |
May 16, 2022 |
| Contact name |
Ming-Jiun Yu |
| E-mail(s) |
mjyu@ntu.edu.tw
|
| Organization name |
National Taiwan University
|
| Department |
Biochemistry and Molecular Biology
|
| Lab |
Systems Biology of Epithelia Laboratory
|
| Street address |
No. 1 Jen-Ai Road Sec. 1, Rm 816
|
| City |
Taipei |
| ZIP/Postal code |
100233 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE194044 |
Glucocorticoid receptor maintains vasopressin responses in kidney collecting duct cells |
|
| Relations |
| BioSample |
SAMN25134303 |
| SRA |
SRX13839656 |
