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Sample GSM4432416 Query DataSets for GSM4432416
Status Public on Jun 09, 2023
Title Organoids scRNA-seq
Sample type SRA
 
Source name iPSC-derived skeletal muscle organoid
Organism Homo sapiens
Characteristics tissue: iPSC-derived skeletal muscle organoid
differentiation stage: 12 weeks
genotype: Wild type iPSCs line
Extracted molecule total RNA
Extraction protocol Organoid 12 weeks post differentiation dissociated into single cells upon incubation for 1hr with solution containing papain and EDTA. Upon dissociation, we estimated the cell number and viability; then cells resuspended on solution containing 0.5% BSA in PBS to reach concentration of 390 cells per ul. The cDNA library was prepared using the Chromium Single Cell 3′ Reagent Kits (v3): Single Cell 3′ Library & Gel Bead Kit v3 (PN-1000075), Single Cell B Chip Kit (PN-1000073) and i7 Multiplex Kit (PN-120262) (10x Genomics).
RNA libraries were prepared for sequencing according to the manufacturers' instructions (10X Genomics).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 3000
 
Data processing illumina bcl2fastq (v2.19.1.403) used for basecalling and demultiplexing
UMI-tools (v1.0.0) used for cell barcode and UMI counting
STAR (v2.7.1a) used for human reference genome (hg38) alignment
Subread featureCounts (v1.6.4) used for UMI quantification
Genome_build: hg38
Supplementary_files_format_and_content: tsv files include UMI counts for each cell barcode and genes
 
Submission date Mar 25, 2020
Last update date Jun 09, 2023
Contact name Hyun-Woo Jeong
E-mail(s) zionjeong@gmail.com
Phone +4917631115236
Organization name Max-Planck-Institute for Molecular Biomedicine
Department Dept. Tissue Morphogenesis
Lab Adams
Street address Roentgenstr.20
City Muenster
State/province NRW
ZIP/Postal code 48149
Country Germany
 
Platform ID GPL21290
Series (2)
GSE147512 Single cell RNA-Seq analysis of human skeletal muscle organoids
GSE147514 Transcriptome profiling of human skeletal muscle organoids
Relations
BioSample SAMN14446531
SRA SRX7992108

Supplementary file Size Download File type/resource
GSM4432416_Org_gene_counts.tsv.gz 67.4 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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