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Sample GSM4096588 Query DataSets for GSM4096588
Status Public on Sep 30, 2020
Title NSC_sgFosl1_1
Sample type SRA
 
Source name NSC_sgFosl1
Organism Mus musculus
Characteristics strain background: mixed
genotype background: GFAP-Tva, LSL_Cas9; Trp53 lox/lox; GFAP-Cre
tissue: brain
cell type: Neural stem cells (NSCs)
treatment: sgFosl1
Growth protocol NSCs were grown in Neurobasal medium, supplemented with EGF and FGF
Extracted molecule total RNA
Extraction protocol Trizol
cDNA libraries were prepared using the "QuantSeq 3‘ mRNA-Seq Library Prep Kit (FWD) for Illumina" (Lexogen, Cat No 015)
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Data processing Sequencing read alignment and quantification and differential gene expression analysis was performed in the Bluebee Genomics Platform, a cloud-based service provider (www.bluebee.com.) Briefly, reads were first trimmed with bbdukfrom BBTools (BBMap –Bushnell B, https://sourceforge.net/projects/bbmap/) to remove adapter sequences and polyA tails. Trimmed reads were aligned to the GRCm38/mm10 genome assembly with STAR v 2.5 (Dobin et al., 2013). Read counting was performed with HTSeq (Anders, Pyl and Huber, 2015).
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Normalized counts
 
Submission date Sep 25, 2019
Last update date Sep 30, 2020
Contact name Massimo Squatrito
E-mail(s) msquatrito@cnio.es
Organization name Spanish National Research Center (CNIO)
Street address Calle Melchor Fernandez Almagro 3
City Madrid
ZIP/Postal code 28029
Country Spain
 
Platform ID GPL17021
Series (1)
GSE138010 Fosl1 regulates mesenchymal GBM plasticity
Relations
BioSample SAMN12842370
SRA SRX6902345

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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