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Sample GSM6900333 Query DataSets for GSM6900333
Status Public on Oct 02, 2023
Title 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: 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-L3XWF
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 SAMN32421874
SRA SRX18859786

Supplementary file Size Download File type/resource
GSM6900333_SM-L3XWF_barcodes.tsv.gz 39.8 Kb (ftp)(http) TSV
GSM6900333_SM-L3XWF_features.tsv.gz 325.6 Kb (ftp)(http) TSV
GSM6900333_SM-L3XWF_matrix.mtx.gz 36.8 Mb (ftp)(http) MTX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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