|
| Status |
Public on Dec 29, 2021 |
| Title |
Cubilin KO clone set 3 |
| Sample type |
SRA |
| |
|
| Source name |
OK_Cubn KO clone
|
| Organism |
Didelphis virginiana |
| Characteristics |
model: proximal tubule cell model
genotype: cubilin knockout
cell type: opossum kidney (OK) cells
|
| Growth protocol |
Control, Cubn KO, Lrp2 KO, and Dab2 KO cells were plated at superconfluence on 12 mm permeable supports in 0.5 mL apical and 1.5 mL basolateral DMEM/F12 medium (Sigma D6421) with 10% FBS (Atlanta Biologicals) and 5 mM GlutaMAX (Gibco). After 18 h (t = 0 h), the filters were transferred to an orbital platform shaker rotating at 146 rpm and the incubation continued for 72 h with daily medium changes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected using Accutase (BD Biosciences) and RNA was extracted using the Ambion PureLink RNA mini kit (Thermo Fisher Scientific). RNA from three independent experiments was sequenced for each clone.
Library preparation and RNA Seq was performed by the University of Pittsburgh School of Medicine Genomics Analysis Core
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
trimmed high quality reads were aligned to genome using TopHat2
Genome_build: https://www.ncbi.nlm.nih.gov/assembly/GCF_000002295.2/
Supplementary_files_format_and_content: raw counts and normalized counts
|
| |
|
| Submission date |
Jun 03, 2021 |
| Last update date |
Dec 29, 2021 |
| Contact name |
B. Rhodes Ford |
| E-mail(s) |
BRF56@pitt.edu
|
| Organization name |
University of Pittsburgh
|
| Department |
Department of Pediatrics
|
| Lab |
Poholek Lab
|
| Street address |
4401 Penn Ave.
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15224 |
| Country |
USA |
| |
|
| Platform ID |
GPL23025 |
| Series (1) |
| GSE176090 |
Cubilin-, Megalin- and Dab2-dependent transcription revealed by CRISPR/Cas9 knockout in kidney proximal tubule cells |
|
| Relations |
| BioSample |
SAMN19548258 |
| SRA |
SRX11052907 |
