|
| Status |
Public on Mar 21, 2024 |
| Title |
P2 129-1 |
| Sample type |
SRA |
| |
|
| Source name |
Nephron progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Nephron progenitor cells
strain: 129S1
genotype: Wild type
age: P2
|
| Growth protocol |
Single-cell suspensions of nephron progenitor cells were isolated by FACS from the kidneys of mice of the indicated strains/timepoints using antibodies for Itga8+, Pdgfra-; and GFP+ if applicable to the sample.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated from purified nephron progenitor cells as described by Buenrostro et al (2013)
ATAC-Seq (Buenrostro et al, 2013)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Raw reads in fastq format were processed using Computational Suite For Bioinformaticians and Biologists (CSBB-v3.0)
Raw reads were mapped to mm10 version of Mouse genome
CSBB uses fastqc for quality check, Bowtie2 for mapping and MACS2 for peak calling
Assembly: mm10
Supplementary files format and content: .bw files were generated and peaks were called using MACS2
|
| |
|
| Submission date |
Feb 02, 2023 |
| Last update date |
Mar 21, 2024 |
| Contact name |
Alison Jarmas Perl |
| Organization name |
CCHMC
|
| Street address |
3333 Burnet Ave.
|
| City |
Cincinnati |
| State/province |
Ohio |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE224324 |
Genome-wide chromatin accessibility (ATAC-Seq) of primary murine nephron progenitor cells. |
|
| Relations |
| BioSample |
SAMN33017034 |
| SRA |
SRX19257605 |
