|
| Status |
Public on Nov 17, 2021 |
| Title |
mIMCD3 DMSO 3D replicate 4 |
| Sample type |
SRA |
| |
|
| Source name |
mouse inner medullary collecting duct cell line
|
| Organism |
Mus musculus |
| Characteristics |
cell line: mIMCD3
tissue: kidney
genotype: wild type
cell type: mouse inner medullary collecting duct cell line
treatment: DMSO
time: 3 days
|
| Treatment protocol |
Cells were grown on the permeable filters of a transwell system (6-well) for 10 days and treated with doxycycline (2 ug/mL) or vehicle (DMSO) for 3 days or 6 days. Media containing doxycycline or vehicle were daily changed.
|
| Growth protocol |
mIMCD3 cells were grown on a permeable filter membrane for 10 days in the RenaLife Epithelial Basal Medium (LM-0010, LIFELINE CELL TECHNOLOGY) supplemented with a RenaLife LifeFactors Kit (LS-1048, LIFELINE CELL TECHNOLOGY) and 5% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lyzed in Trizol. Total RNA was extracted using Direct-zol RNA Miniprep kit (ZYMO RESEARCH).
To enrich mRNA, 1-3 ug of total RNA was applied to oligo dT-based mRNA isolation using NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490, NEW ENGLAND BioLabs Inc.) as a manufacturer’s instruction. mRNA (20-30 ng) was sequentially used for the further sequencing library preparation using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760, NEW ENGLAND BioLabs Inc.) and NEBNext® Multiplex Oligos (E7335; E7500, NEW ENGLAND BioLabs Inc.). cDNA libraries were sequenced on Illumina HiSeq 4000 platform. Sequence reads (2 × 75 bp, paired-end) were aligned on Ensembl genome GRCm38p6 using STAR (2.6.0c).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
DMSO_3D_4
|
| Data processing |
Four technical repliates of each experimental group were prepared for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 using salmon (0.14.10).
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 06, 2021 |
| Last update date |
Nov 17, 2021 |
| Contact name |
Hyun Jun Jung |
| E-mail(s) |
[email protected]
|
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
Medicine (Nephrology)
|
| Street address |
720 Rutland Ave, Ross Research Building 1165B
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE171573 |
Doxycycline-responsive transcriptome in the mouse inner medullary collecting duct cell line (mIMCD3) |
|
| Relations |
| BioSample |
SAMN18633904 |
| SRA |
SRX10522730 |
