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Sample GSM5849415 Query DataSets for GSM5849415
Status Public on May 05, 2023
Title SC_low_passage
Sample type SRA
 
Source name SC_young
Organism Homo sapiens
Characteristics tissue: hPSC-derived Schwann Cell culture
cell line source: H9
plating: attached
Growth protocol Low and high passage Schwann cells were differentiated from hPSC-derived neural crest cells and grown in Schwann Cell Medium (Sciencell, 1701).
Extracted molecule total RNA
Extraction protocol Cells were washed with PBS and detached using trypsin. The enzyme was quenched with media containing 2% FBS and washed away by extra media followed by PBS. Cells were passed through a 37μm reversible cell strainer and put on ice. Before submission for library prep.
snRNA-seq libraries were prepared with Chromium Next GEM Single Cell 3′ Kit v3.1 (10x Genomics). The libraries were sequenced at UCSF GenomicsCoLab.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Transcript Quantification: FASTA (fasta.gz) files were quantified using CellRanger. The specific command was 'cellranger count' with parameters '--include-introns --nosecondary' all other paramters were default.
Preprocessing: filtered count matrices fromCellRanger were read into R and processed using Seurat (v4.0.4). The reminaing cells were filtered for total genes, total umis and mitochondrial percentage.
Analysis: Sample were analysed using Seurat's standard workflow.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed data is provided as (.csv) files and contain a gene count matrix of cell IDs post CellRanger filtering pre Seurat filtration.
 
Submission date Jan 30, 2022
Last update date May 05, 2023
Contact name Faranak Fattahi
E-mail(s) fattahilab@gmail.com
Organization name University of California San Francisco
Department Cellular and Molecular Pharmacology
Lab Fattahi Lab
Street address 600 16th St
City San Francisco
State/province California
ZIP/Postal code 94143
Country USA
 
Platform ID GPL24676
Series (1)
GSE195730 Deriving Schwann Cells from hPSCs Enable Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy
Relations
BioSample SAMN25487969
SRA SRX13991285

Supplementary file Size Download File type/resource
GSM5849415_sc.young.counts.csv.gz 49.0 Mb (ftp)(http) CSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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