NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7100734 Query DataSets for GSM7100734
Status Public on May 05, 2023
Title psc2, primary Schwann cell, replicate 2
Sample type SRA
 
Source name Schwann cell
Organism Homo sapiens
Characteristics 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
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 GPL20301
Series (1)
GSE195730 Deriving Schwann Cells from hPSCs Enable Disease Modeling and Drug Discovery for Diabetic Peripheral Neuropathy
Relations
BioSample SAMN33772520
SRA SRX19685646

Supplementary file Size Download File type/resource
GSM7100734_PSC2_sorted_hg19_HTSEQ.txt.gz 123.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap