|
| Status |
Public on May 08, 2024 |
| Title |
SHAM 10 days |
| Sample type |
SRA |
| |
|
| Source name |
Whole kidney 10 days post SHAM
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
age: adult 12 weeks
Sex: Male
|
| Treatment protocol |
12 weeks mice males were subjected to UUO or SHAM. After 10 days, obstructed kidneys or SHAM control were harvested and single-cell RNA-seq was performed on the whole kidney.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Kidneys were collected and subjected to single cell disregation protocol as described in Youssef et al. 2021.
Single cell preprartion from whole kidney were processed to generate cDNA libraries according to Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 protocol (10X Genomics). Pooled libraries were then loaded on a HiSeq2500 instrument (Illumina) and sequenced to obtain 75 bp paired-end reads.
scRNA-seq (single-cell RNA-seq)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
single-cell gene expression profiling (scRNA-seq)
|
| Data processing |
Sequencer: Illumina HiSeq 2500. Basecalling pipeline: HiSeq Control Software [[2.2.58]]. HiSeq Sequencing v4 Chemistry. Read Length: 75 paired end
Quality control of sequenced reads was performed using FastQC (Babraham Institute). Sequenced samples were processed using the Cell Ranger (v.2.2.0) pipeline (10x Genomics) and aligned to the CRGm38 (mm10) mouse reference genome customized to also count reads in WPRE exogenous sequence as a cancer cell tdTomato reporter (gene annotation version 99. We retrieved 310M reads per sample, 61% reads mapped confidently to exonic regions, 9K mean cells per sample, 34K mean reads per cell, 2.7K mean median unique counts per cell and sample, and 1.1K mean median genes per cell and sample.
Genome_build: GRCm38.99
Supplementary_files_format_and_content: Single-cell RNA-seq datasets. Each dataset contain three files: barcodes.tsv (a tab separated values file with cellular barcodes present in dataset); genes.tsv (a tab separated values file with IDs of quantified genes (Mouse ENSEMBL Gene ID and Gene Symbol); matrix.mtx (a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes). A standard or sparse matrix can be generated where genes.tsv file correspond to the genes or row names of the matrix, while barcodes.tsv corresponds to the cell or columns.
|
| |
|
| Submission date |
May 24, 2021 |
| Last update date |
May 08, 2024 |
| Contact name |
Angela Nieto |
| E-mail(s) |
anieto@umh.es
|
| Organization name |
Instituto de Neurociencias (CSIC-UMH)
|
| Department |
Developmental Neurobiology
|
| Lab |
Cell plasticity in development and disease
|
| Street address |
Av. Ramón y Cajal s/n
|
| City |
San Juan de Alicante |
| State/province |
Alicante |
| ZIP/Postal code |
03550 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE175412 |
Single-cell RNA sequencing of adult mouse fibrotic kidney induced by unilateral uretral obstruction |
|
| Relations |
| BioSample |
SAMN19316757 |
| SRA |
SRX10971460 |
