|
| Status |
Public on Oct 02, 2023 |
| Title |
Day 25 OS-HLOs, replicate 1, scRNAseq |
| Sample type |
SRA |
| |
|
| Source name |
Human liver organoid (HLO)
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Human liver organoid (HLO)
cell line: W01, WiCell
cell type: hPSC-derived HLOs
genotype: Wild-type
treatment: None
time: day 25
|
| Treatment protocol |
OS-HLOs were treated for 5 days with TGF-β1 (10 ng/ml) or PA (500 µM).
|
| Growth protocol |
HLOs were generated from hPSCs. ULA-HLOs were grown for 21 or 34 days. OS-HLOs were cultured for 20 days before undergoing 5 days of treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly collected human liver organoids were washed 1X with warm DPBS(-/-) and briefly dissociated by incubation with 0.05-0.25% Trypsin-EDTA for 10 minutes at 37°C. Day 34 ULA- and day 25 OS-HLOs underwent an additional DBPS (-/-) wash and 10 minutes of trypsinization to allow complete digestion. For each replicate, full single cell dissociation was confirmed manually by light microscopy. After a final DPBS(-/-) wash, organoids were resuspended in DPBS(-/-), counted after with the TC20™ Automated Cell Counter (Trypan Blue) and transferred on ice for library preparation.
Library was performed according to the manufacturer’s instructions (single cell 3’ v3 protocol, 10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
SM-L3XWE
10x Genomics
|
| Data processing |
Raw bcl files were converted to fastq by the command bcl2fastq --use-bases-mask Y26,I8,Y98. Demultiplexing, barcoded processing, gene counting, aggregation and alignment to the GRCh38 genome was performed with the cellranger software version 3.0.2. Downstream analysis was performed in python (version => 3.6) with scanpy version => 1.7.2.
Assembly: GRCh38 (human)
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx).
|
| |
|
| Submission date |
Dec 27, 2022 |
| Last update date |
Oct 02, 2023 |
| Contact name |
Alan C. Mullen |
| E-mail(s) |
mullenlabmgh@gmail.com
|
| Organization name |
Massachusetts General Hospital
|
| Department |
Department of Medicine
|
| Street address |
55 Fruit St.
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02135 |
| Country |
USA |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE207889 |
Stem cell-derived human liver organoids to model the progression of inflammatory and fibrotic injury in non-alcoholic fatty liver disease |
|
| Relations |
| BioSample |
SAMN32421875 |
| SRA |
SRX18859785 |
