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Sample GSM3763147 Query DataSets for GSM3763147
Status Public on Dec 15, 2020
Title Uchimura organoid
Sample type SRA
Source name iPS cells
Organism Homo sapiens
Characteristics protocol: 10x Genomics 5' library kit
tissue: Uchimura 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
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
BioSample SAMN11634514
SRA SRX5824099

Supplementary file Size Download File type/resource
GSM3763147_Uchimura.dge.txt.gz 35.1 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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