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Sample GSM7100738 Query DataSets for GSM7100738
Status Public on May 05, 2023
Title sc5, day 50 differentiation, replicate 2
Sample type SRA
Source name H9
Organism Homo sapiens
Characteristics cell line: H9
cell type: Schwann cell
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using trizol.
First strand cDNA was synthesized with Quantseq Forward Libray preparation kit from Lexogen.
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Data processing Illumina compatible RNA sequencing libraries were prepared with Quantseq and pooled and sequenced on Illumina Hiseq 4000 platform.
UMIs were extracted from the fastq files with umi_tools, and cutadapt was used to remove short and low-quality reads.
RNA-seq reads were mapped to the human reference genome (hg19) using TopHat v2.0. TopHat was run with default parameters with exception to the coverage search. Alignments were then quantified using HTSeq.
Duplicate reads were collapsed using umi_tools. Gene level counts were measured using HTSeq and compared using DESeq2.
Assembly: GRCh38
Submission date Mar 15, 2023
Last update date May 05, 2023
Contact name Faranak Fattahi
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 GPL20301
Series (1)
GSE195730 Deriving Schwann Cells from hPSCs Enable Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy
BioSample SAMN33772516
SRA SRX19685650

Supplementary file Size Download File type/resource
GSM7100738_SC5_sorted_hg19_HTSEQ.txt.gz 125.0 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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