|
| Status |
Public on Mar 14, 2024 |
| Title |
iNPC derived organoid, Replicate 2 d21, ATAC Library |
| Sample type |
SRA |
| |
|
| Source name |
Kidney organoids
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney organoids
cell type: Kidney cells
genotype: SIX2-GFP/PAX2-RFP
treatment: Kidney organoids were cultured with Stage III medium
|
| Growth protocol |
Kidney organoids were cultured with Stage III medium (Advanced RPMI 1640 medium with 1X B27 and 200nM A83-01), 37C, 5% CO2
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Orgnaoids were miccrodissected and digested in CAP digestion solution (10mg/ml Cold Active Protease+ 2.5 mg/ml Collagenase type 4 + 0.125U/ul Dnase1) at 12°C for 30 mins. Cells were then spun down at 350G for 5 mins and resuspended in cold autoMACS Running Buffer. Cell viablity was accessed (99% Live) and cells spun down again. 10X genomics Demonstarated Proocol CG000365 (REV C) was then used to isolate nuclei with 5 min lysis time. The single nuclei suspension was than transposed and run through a microfuidic chip (Chip J) for barcoding.
10X Chromium Single Cell Multiome + Gene Expression protocol (CG000338 Rev E)
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ATAC_iNPC2
10X Chromium multiome ATAC + gene expression kit
|
| Data processing |
Sequencing reads were aligned to the human genome (GRCh38) with the Cell Ranger ARC software (version 2.0.2) using STAR aligner on the University of Southern California High Performance Cluster.
Assembly: arc-GRCh38-2020-A-2.0.0
Supplementary files format and content: atac_fragaments_tsv.gz, Tab-separated file containing fragment information
Supplementary files format and content: atac_fragaments_tsv.gz.tbi, Index of the tab-separated file
Supplementary files format and content: H5 file containing the filtered gene by cell gene expression and peak by cell matrices
Library strategy: snRNA-seq + snATAC-seq
|
| |
|
| Submission date |
Dec 21, 2023 |
| Last update date |
Mar 14, 2024 |
| Contact name |
Kari Ann Koppitch |
| E-mail(s) |
[email protected]
|
| Organization name |
USC
|
| Department |
Stem Cell
|
| Lab |
McMahon
|
| Street address |
1425 San Pablo Street, BCC 312
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033-9080 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE251862 |
Modeling kidney development, disease, and plasticity with clonal expandable nephron progenitor cells and nephron organoids |
|
| Relations |
| BioSample |
SAMN39058767 |
| SRA |
SRX22998059 |
