|
| Status |
Public on Dec 15, 2020 |
| Title |
Takasato organoid |
| Sample type |
SRA |
| |
|
| Source name |
iPS cells
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: 10x Genomics 5' library kit
tissue: Takasato organoid
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Organoids from Uchimura and Takasato protocols were harvested at day 26 and dissociated into single cells using 0.25% TrypLE. Cells were counted on hemocytometers (InCYTO C-chip) and partitioned into each droplet with a barcoded gel bead using the 10X Chromium instrument (10X Genomics, Pleasanton, CA). Single cell was lysed and RNAs were reverse transcribed into cDNA within each droplet. After breaking the emulsion, cDNAs were amplified and fragmented followed by the addition of Illumina adapters using the Chromium Single Cell 5’ Library & Gel Bead Kit. Samples were indexed and sequenced on the S4 flow cell of NovaSeq 6000 (Illumina).
RNA libraries were prepared for sequencing following the 5' library preparation protocol from 10x Genomics
10x Chromium 5' scRNA-seq library
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
single cell RNA-seq
|
| Data processing |
Raw reads were demultiplexed using the command “cellranger mkfastq” from the CellRanger toolkit (version 3.0). Read alignment, barcode identification and UMI quantification were completed using the command “cellranger count”.
Genome_build: GRCh38
Supplementary_files_format_and_content: cellranger count
|
| |
|
| Submission date |
May 13, 2019 |
| Last update date |
Dec 19, 2020 |
| Contact name |
Haojia Wu |
| E-mail(s) |
haojiawu@wustl.edu
|
| Organization name |
Washington University in St. Louis
|
| Department |
Renal Division/Internal Medicine
|
| Lab |
Humphreys Lab
|
| Street address |
600 S Euclid Ave
|
| City |
St. Louis |
| State/province |
Missouri |
| ZIP/Postal code |
MO 63110 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE131086 |
Human Pluripotent Stem Cell-Derived Kidney Organoids for Modeling Epithelial Transport and Injury |
|
| Relations |
| BioSample |
SAMN11634515 |
| SRA |
SRX5824098 |
