NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM5354859 Query DataSets for GSM5354859
Status Public on Dec 29, 2021
Title Dab2 KO clone set 1
Sample type SRA
 
Source name OK_Dab2 KO clone
Organism Didelphis virginiana
Characteristics model: proximal tubule cell model
genotype: Dab2 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 SAMN19548254
SRA SRX11052911

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap