|
| Status |
Public on Aug 10, 2023 |
| Title |
Stab-12-5-3 |
| Sample type |
SRA |
| |
|
| Source name |
CD1_β-catSO_E12.5
|
| Organism |
Mus musculus |
| Characteristics |
strain background: CD1
genotype: beta-catSO
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 |
Stab-12-5-3_S15_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 |
SAMN15785141 |
| SRA |
SRX8923883 |
