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Sample GSM6322580 Query DataSets for GSM6322580
Status Public on Oct 02, 2023
Title PA-500 µM treated day 25 OS-HLOs, replicate 2, 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: PA 500 µM
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 manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics).
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description 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 or 6.0.2. 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 Jul 11, 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 GPL24676
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 SAMN29630403
SRA SRX16114858

Supplementary file Size Download File type/resource
GSM6322580_SM-KBV65_barcodes.tsv.gz 45.3 Kb (ftp)(http) TSV
GSM6322580_SM-KBV65_features.tsv.gz 297.6 Kb (ftp)(http) TSV
GSM6322580_SM-KBV65_matrix.mtx.gz 68.6 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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