NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4720567 Query DataSets for GSM4720567
Status Public on Aug 10, 2023
Title K-O-con-12-5-2
Sample type SRA
 
Source name C57BL/6_wild-type_E12.5
Organism Mus musculus
Characteristics strain background: C57BL/6
genotype: wild-type
developmental stage: E12.5
tissue: kidney
cell type: stromal cells
Extracted molecule total RNA
Extraction protocol Embryonic kidneys were micro-dissected using Dumont #5 INOX surgical forceps in cold phosphate-buffered saline (PBS) pH 7.4 under a Leica EZ4D microscope and were washed in cold PBS immediately after microdissection. Kidney explants were dissociated using 0.3% Collagenase (Sigma Aldrich) for 10 minutes at 37°C. Kidneys were then triturated through a 25-gauge needle to make a single-cell suspension, and then washed 3 times in cold PBS supplemented with 2% fetal bovine serum. Before sorting, cells were run through a 40μm strainer (ThermoFisher Scientific). Cells were sorted into PBS (if undergoing second sort) or directly into Qiagen’s RLT Lysis Buffer.
Sequencing of samples was performed using the Illumina HiSeq system (Illumina, San Diego).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description K-O-con-12-5-2_S8_L001
Data processing Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to the UCSC/mm10 reference version using HISAT2.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data file contains a matrix containing data from all samples.
 
Submission date Aug 11, 2020
Last update date Aug 10, 2023
Contact name Darreb Bridgewater
E-mail(s) bridgew@mcmaster.ca, erin_deacon@hotmail.com
Organization name McMaster University
Street address 1280 Main Street West
City Hamilton
State/province Ontario
ZIP/Postal code L8S 4K1
Country Canada
 
Platform ID GPL18480
Series (1)
GSE156022 RNA-seq of mouse embryonic kidney stromal cells with stabilized or deficient β-catenin expression
Relations
BioSample SAMN15785064
SRA SRX8923876

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