|
| Status |
Public on Jun 20, 2024 |
| Title |
15.6 Wk human fetal, snRNA-seq, rep F3 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Kidney tissue
cell type: Kidney cells
age: 15.6 Wk human fetal
treatment: N/A
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Cryopreserved human fetal kidneys were processed with optimized single-nuclei dissociation protocol to minimize potential tissue damage artifacts from frozen samples and loss of intact RNA molecules during the dissociation process. Briefly, the tissues were transported in DMEM (5% FBS, 25mM HEPES), removed from capsules, dissected into <2mm pieces and flash frozen in liquid nitrogen for later isolation. Nuclei isolation from flash frozen tissue was performed by the same protocol used with mouse tissue described above. For sex identification, a small amount of the donor tissue was lysed, and DNA was isolated by incubating in DirectPCR Lysis Reagent (Qiagen, #102-T) with 1% Proteinase K (Roche, 3115879001). Donor tissue was then sexed using primers for Y-specific human SRY (SRY-FOR: CCC ATG AAC GCA TTC ATT GTG TGG/ SRY-REV: ATT TTA GCC TTC CGA CGA GGT CGA TA), and ZFX/ZFY (ZFX/ZFY FOR: GCA CTT CTT TGG TAT CTG AGA AAG T/ ZFX/ZFY REV: ATA ATC ACA TGG AGA GCC ACA AGC T) to confirm DNA isolation quality.
Chromium_SingleCell_3'_ReagentKits_v3_UserGuide (CG000183)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
10X Chromium Single Cell 3' v3
|
| Data processing |
Sequencing reads were aligned to the human genome (GRCh38-2020-A) with the Cell Ranger software (version 5.0.1) using STAR aligner on the University of Southern California High Performance Cluster. The samples were aggregated using cellranger aggr. The processed files (filtered_feature_bc_matrix.h5) are provided. Controlled access to raw fastq files is available through dbGaP.
Assembly: GRCh38-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.h5
|
| |
|
| Submission date |
May 13, 2023 |
| Last update date |
Jun 20, 2024 |
| Contact name |
Andrew P McMahon |
| E-mail(s) |
amcmahon@med.usc.edu
|
| Phone |
323-442-7847
|
| Organization name |
University of Southern California
|
| Department |
Stem Cell Biol & Regen Med
|
| Lab |
Andrew McMahon
|
| Street address |
1425 San Pablo St, BCC 312
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE232479 |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development [human snRNA-seq] |
| GSE232482 |
Comparative single-cell analyses identify shared and divergent features of human and mouse kidney development |
|
